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value | identifier stringlengths 1 71 | return_type stringlengths 1 749 ⌀ | original_string stringlengths 76 22.7k | original_docstring stringlengths 16 7.61k | docstring stringlengths 16 2.47k | docstring_tokens listlengths 6 477 | code stringlengths 14 10.2k | code_tokens listlengths 6 996 | short_docstring stringlengths 2 644 | short_docstring_tokens listlengths 1 116 | comment listlengths 1 89 | parameters listlengths 0 64 | docstring_params dict |
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535f6fccc44bf532f1700aba30493c21b723a489 | shambo001/peat | PEATDB/DNAtool/DNAtool.py | [
"MIT"
] | Python | load_preferences | <not_specific> | def load_preferences(self):
"""Loads the sequence display settings from prefs file, if present"""
print 'Loading current DNAtool preferences'
self.preferences = Preferences('DNAtool',{'canvas_height':600})
for key in self.defaultprefs:
if key in self.preferences.prefs:
... | Loads the sequence display settings from prefs file, if present | Loads the sequence display settings from prefs file, if present | [
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"display",
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"from",
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"file",
"if",
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] | def load_preferences(self):
print 'Loading current DNAtool preferences'
self.preferences = Preferences('DNAtool',{'canvas_height':600})
for key in self.defaultprefs:
if key in self.preferences.prefs:
self.__dict__[key].set(self.preferences.get(key))
else:
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} |
535f6fccc44bf532f1700aba30493c21b723a489 | shambo001/peat | PEATDB/DNAtool/DNAtool.py | [
"MIT"
] | Python | update_window_formatting | <not_specific> | def update_window_formatting(self):
"""Do this only when display setup changes are applied. Ensures all objects, including
applied primers are updated with the new formatting."""
self.update_sequence_window()
if self.pDB_open:
self.pDB_open.refresh_primer()
if self.... | Do this only when display setup changes are applied. Ensures all objects, including
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] | def update_window_formatting(self):
self.update_sequence_window()
if self.pDB_open:
self.pDB_open.refresh_primer()
if self.show_comp_sequence.get==1:
self.sequ_win.refresh_DNAseq()
return | [
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535f6fccc44bf532f1700aba30493c21b723a489 | shambo001/peat | PEATDB/DNAtool/DNAtool.py | [
"MIT"
] | Python | overview_on_off | <not_specific> | def overview_on_off(self):
"""Turn the over view window on and off"""
if self.overview_win:
self.overview_button.deselect()
self.overview_win.destroy()
self.overview_win=None
else:
self.overview_button.select()
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] | def overview_on_off(self):
if self.overview_win:
self.overview_button.deselect()
self.overview_win.destroy()
self.overview_win=None
else:
self.overview_button.select()
if not self.data.has_key('AA_seqs1'):
self.warning('No DNA s... | [
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} |
535f6fccc44bf532f1700aba30493c21b723a489 | shambo001/peat | PEATDB/DNAtool/DNAtool.py | [
"MIT"
] | Python | compare_DNA_seq | <not_specific> | def compare_DNA_seq(self):
"""load and display a sequence from a file to compare to the currently
displayed sequence"""
import tkMessageBox
if self.data['DNAseq']=='' or not self.data['DNAseq']:
tkMessageBox.showwarning(
"Compare DNA Sequence",
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] | def compare_DNA_seq(self):
import tkMessageBox
if self.data['DNAseq']=='' or not self.data['DNAseq']:
tkMessageBox.showwarning(
"Compare DNA Sequence",
"Load a DNA sequence first\nUse the Browse Button"
)
return
else:
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} |
535f6fccc44bf532f1700aba30493c21b723a489 | shambo001/peat | PEATDB/DNAtool/DNAtool.py | [
"MIT"
] | Python | compare_multiple_seqs | <not_specific> | def compare_multiple_seqs(self):
"""load and display many sequences in a set of files or zip file"""
import tkMessageBox
if self.data['DNAseq']=='' or not self.data['DNAseq']:
tkMessageBox.showwarning(
"Compare DNA Sequence",
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] | def compare_multiple_seqs(self):
import tkMessageBox
if self.data['DNAseq']=='' or not self.data['DNAseq']:
tkMessageBox.showwarning(
"Compare DNA Sequence",
"Load a DNA sequence first\nUse the Browse Button"
)
return
else:
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} |
535f6fccc44bf532f1700aba30493c21b723a489 | shambo001/peat | PEATDB/DNAtool/DNAtool.py | [
"MIT"
] | Python | clear_comp_seqs | <not_specific> | def clear_comp_seqs(self, event=None):
"""switch off display of extra comparison sequences"""
self.show_comp_sequence.set(0)
print 'clearing comp seq'
self.seqframe.delete('comparison_seq')
self.seqframe.delete('strip')
self.max_seq_level=0
self.update_sequence_w... | switch off display of extra comparison sequences | switch off display of extra comparison sequences | [
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"display",
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"sequences"
] | def clear_comp_seqs(self, event=None):
self.show_comp_sequence.set(0)
print 'clearing comp seq'
self.seqframe.delete('comparison_seq')
self.seqframe.delete('strip')
self.max_seq_level=0
self.update_sequence_window()
if self.pDB_open:
self.pDB_open.refr... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | resnum | <not_specific> | def resnum(self,uniqueid):
"""Given a uniqueid this function returns the residue number"""
import string
if len(string.split(uniqueid,','))>1:
return string.split(uniqueid,':')[0]+':'+string.zfill(string.split(uniqueid,':')[1],self.length_of_residue_numbers)+','+string.split(uniqueid... | Given a uniqueid this function returns the residue number | Given a uniqueid this function returns the residue number | [
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import string
if len(string.split(uniqueid,','))>1:
return string.split(uniqueid,':')[0]+':'+string.zfill(string.split(uniqueid,':')[1],self.length_of_residue_numbers)+','+string.split(uniqueid,',')[1]
else:
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | resname | <not_specific> | def resname(self,uniqueid):
""" Given an uniqueid or a residue number, this function returns the residue name"""
import string
if self.atoms.has_key(uniqueid):
return self.atoms[uniqueid]['RESNAME']
elif self.residues.has_key(uniqueid):
#
# Get the fir... | Given an uniqueid or a residue number, this function returns the residue name | Given an uniqueid or a residue number, this function returns the residue name | [
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] | def resname(self,uniqueid):
import string
if self.atoms.has_key(uniqueid):
return self.atoms[uniqueid]['RESNAME']
elif self.residues.has_key(uniqueid):
Get the first atom of the residue and return the resname there
atomname=self.residues[uniqueid][0]
... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | NextResidue | <not_specific> | def NextResidue(self,resid,checkforbound=1):
"""
# This function returns the residue one after resid in the sequence in the same molecule
# This function only works for amino acids
"""
if not self.isaa(resid):
raise NotAnAminoAcidError('%s %s' %(resid,self.resname(res... |
# This function returns the residue one after resid in the sequence in the same molecule
# This function only works for amino acids
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] | def NextResidue(self,resid,checkforbound=1):
if not self.isaa(resid):
raise NotAnAminoAcidError('%s %s' %(resid,self.resname(resid)))
Make sure we get rid of all ',ALT' records in the name when skipping residues
resid=resid.replace(',ALT','')
residues=self.residues.keys()
... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | GetPosition | <not_specific> | def GetPosition(self,uniqueid):
"""
# This function loads the X, Y and Z coordinates of the atom
# in an Numeric Python vector
"""
if not self.atoms.has_key(uniqueid):
raise AtomNotFoundError,uniqueid
if not self.atoms[uniqueid].has_key('X') or not self.atoms[... |
# This function loads the X, Y and Z coordinates of the atom
# in an Numeric Python vector
| This function loads the X, Y and Z coordinates of the atom
in an Numeric Python vector | [
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] | def GetPosition(self,uniqueid):
if not self.atoms.has_key(uniqueid):
raise AtomNotFoundError,uniqueid
if not self.atoms[uniqueid].has_key('X') or not self.atoms[uniqueid].has_key('Y') or not self.atoms[uniqueid].has_key('Z'):
print self.atoms[uniqueid]
raise Incomplet... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | SetPosition | <not_specific> | def SetPosition(self,uniqueid,coords):
"""Set the coordinates of this atom"""
if not self.atoms.has_key(uniqueid):
raise AtomNotFoundError,uniqueid
self.atoms[uniqueid]['X']=coords[0]
self.atoms[uniqueid]['Y']=coords[1]
self.atoms[uniqueid]['Z']=coords[2]
ret... | Set the coordinates of this atom | Set the coordinates of this atom | [
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] | def SetPosition(self,uniqueid,coords):
if not self.atoms.has_key(uniqueid):
raise AtomNotFoundError,uniqueid
self.atoms[uniqueid]['X']=coords[0]
self.atoms[uniqueid]['Y']=coords[1]
self.atoms[uniqueid]['Z']=coords[2]
return | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | add_atom | <not_specific> | def add_atom(self,uniqueid,
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chainid='X',residuename='DUM',residuenumber='000',
xcoord=0.0,ycoord=0.0,zcoord=0.0,update=1,BFACTOR=None,OCCUPANCY=None,CHARGE=None,RADIUS=None,tag=None,accept_duplicate=False):
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xcoord=0.0,ycoord=0.0,zcoord=0.0,update=1,BFACTOR=None,OCCUPANCY=None,CHARGE=None,RADIUS=None,tag=None,accept_duplicate=False):
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | remove_residue | <not_specific> | def remove_residue(self,unique_identifier,update=True):
"""Remove a residue. This includes deleted all atoms in the residue"""
if not self.residues.has_key(unique_identifier):
raise ResidueNotFoundError(unique_identifier)
for atom in self.residues[unique_identifier]:
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if not self.residues.has_key(unique_identifier):
raise ResidueNotFoundError(unique_identifier)
for atom in self.residues[unique_identifier]:
self.remove_atom(atom,update=False)
if update:
self.Update()
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | Remove_All_NonAminoAcids | <not_specific> | def Remove_All_NonAminoAcids(self):
"""Remove all non amino acid residues"""
for residue in self.residues.keys():
if not self.isaa(residue):
for atom in self.residues[residue]:
del self.atoms[atom]
self.Update()
return | Remove all non amino acid residues | Remove all non amino acid residues | [
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] | def Remove_All_NonAminoAcids(self):
for residue in self.residues.keys():
if not self.isaa(residue):
for atom in self.residues[residue]:
del self.atoms[atom]
self.Update()
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | remove_atoms_with_tag | <not_specific> | def remove_atoms_with_tag(self,tag=''):
"""Remove all atoms with the specified tag"""
for atom in self.atoms.keys():
if self.atoms[atom].has_key('tag'):
if self.atoms[atom]['tag']==tag:
self.remove_atom(atom)
return | Remove all atoms with the specified tag | Remove all atoms with the specified tag | [
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for atom in self.atoms.keys():
if self.atoms[atom].has_key('tag'):
if self.atoms[atom]['tag']==tag:
self.remove_atom(atom)
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | make_boxes | <not_specific> | def make_boxes(self):
"""Divide all atoms into 6A boxes"""
self.boxes={}
self.small_boxes={}
for atom in self.atoms:
x_index=int(self.atoms[atom]['X']/6.0)
y_index=int(self.atoms[atom]['Y']/6.0)
z_index=int(self.atoms[atom]['Z']/6.0)
index=... | Divide all atoms into 6A boxes | Divide all atoms into 6A boxes | [
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] | def make_boxes(self):
self.boxes={}
self.small_boxes={}
for atom in self.atoms:
x_index=int(self.atoms[atom]['X']/6.0)
y_index=int(self.atoms[atom]['Y']/6.0)
z_index=int(self.atoms[atom]['Z']/6.0)
index='%d_%d_%d' %(x_index,y_index,z_index)
... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | hasMissingMainChainAtoms | <not_specific> | def hasMissingMainChainAtoms(self):
"""Check that each amino acid residue has all heavy main chain atoms"""
missing=[]
for residue in self.residues.keys():
if not self.isaa(residue):
continue
for atom in ['O','C','CA','N']:
if not '%s:%s' %... | Check that each amino acid residue has all heavy main chain atoms | Check that each amino acid residue has all heavy main chain atoms | [
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missing=[]
for residue in self.residues.keys():
if not self.isaa(residue):
continue
for atom in ['O','C','CA','N']:
if not '%s:%s' %(residue,atom) in self.residues[residue]:
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} |
b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | hasChainBreak | <not_specific> | def hasChainBreak(self):
"""Check if the soup contains chains with chain breaks"""
for chain in self.chains.keys():
residues=sorted(self.chains[chain])
Cterms=0
Nterms=0
for residue in residues:
if not self.isaa(residue):
... | Check if the soup contains chains with chain breaks | Check if the soup contains chains with chain breaks | [
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for chain in self.chains.keys():
residues=sorted(self.chains[chain])
Cterms=0
Nterms=0
for residue in residues:
if not self.isaa(residue):
continue
try:
nextres=self.N... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | readpdb | <not_specific> | def readpdb(self,filename=None,data=None,parse=1,readmodels=1,use_NMRnumber=True):
"""
# Reads a pdb file and lets PDBparser.parse do the parsing
"""
import os
if data != None:
import StringIO
stream = StringIO.StringIO(data)
self.l... |
# Reads a pdb file and lets PDBparser.parse do the parsing
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import os
if data != None:
import StringIO
stream = StringIO.StringIO(data)
self.lines = stream.readlines()
elif os.path.isfile(filename):
if... | [
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | renumber_atoms | <not_specific> | def renumber_atoms(self):
"""Renumber all atoms based on their names"""
count=0
atoms=self.atoms.keys()
atoms.sort()
for atom in atoms:
self.atoms[atom]['NUMBER']=count+1
count=count+1
return | Renumber all atoms based on their names | Renumber all atoms based on their names | [
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] | def renumber_atoms(self):
count=0
atoms=self.atoms.keys()
atoms.sort()
for atom in atoms:
self.atoms[atom]['NUMBER']=count+1
count=count+1
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | writepdb | <not_specific> | def writepdb(self,filename,header=None,nowrite=False,dont_write_HETATMS=None,TER=1,pqr=None,style=None):
"""
# Writes a PDB file from the informations in self.atoms
"""
#
# Renumber all atoms first
#
self.renumber_atoms()
#
# Write the file
... |
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Renumber all atoms first
self.renumber_atoms()
Write the file
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def __init__(self):
self.lines=[]
def write(self,text):
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | parsepdb | <not_specific> | def parsepdb(self,lines):
"""
Parses a PDB file, which is contained in lines (a list of lines)
"""
import PDBparser
Y=PDBparser.PDBparser(lines,self.parse_terms)
Y.parse()
self.atoms=Y.atoms
self.Update()
self.attribute=Y.attribute
... |
Parses a PDB file, which is contained in lines (a list of lines)
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] | def parsepdb(self,lines):
import PDBparser
Y=PDBparser.PDBparser(lines,self.parse_terms)
Y.parse()
self.atoms=Y.atoms
self.Update()
self.attribute=Y.attribute
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b3736aea4b37ecf8a47ec3361bdb188dcfb75f73 | shambo001/peat | Protool/structure.py | [
"MIT"
] | Python | addpdblines | <not_specific> | def addpdblines(self,lines):
"""Add the atoms in lines to the current set of atoms"""
import PDBparser
Y=PDBparser.PDBparser(lines,self.parse_terms)
Y.parse()
error=False
for atom in Y.atoms.keys():
if not self.atoms.has_key(atom):
self.atoms[a... | Add the atoms in lines to the current set of atoms | Add the atoms in lines to the current set of atoms | [
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] | def addpdblines(self,lines):
import PDBparser
Y=PDBparser.PDBparser(lines,self.parse_terms)
Y.parse()
error=False
for atom in Y.atoms.keys():
if not self.atoms.has_key(atom):
self.atoms[atom]=Y.atoms[atom]
else:
print 'Name ... | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | mult_calc_anal | <not_specific> | def mult_calc_anal(self,event=None):
"""Open the multiple calc analysis window"""
import multiple_calc_analysis
multiple_calc_analysis.multiple_calc_analysis(self)
return | Open the multiple calc analysis window | Open the multiple calc analysis window | [
"Open",
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] | def mult_calc_anal(self,event=None):
import multiple_calc_analysis
multiple_calc_analysis.multiple_calc_analysis(self)
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | add_to_pulldown | <not_specific> | def add_to_pulldown(self,pdbfilename,label):
"""Add a new titration to the menus"""
self.calc_disp[pdbfilename]=IntVar()
self.display_menu.add_checkbutton(label=label+':'+pdbfilename,
variable=self.calc_disp[pdbfilename],
... | Add a new titration to the menus | Add a new titration to the menus | [
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] | def add_to_pulldown(self,pdbfilename,label):
self.calc_disp[pdbfilename]=IntVar()
self.display_menu.add_checkbutton(label=label+':'+pdbfilename,
variable=self.calc_disp[pdbfilename],
onvalue=1,offvalue=0,
... | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | update_all_groups | <not_specific> | def update_all_groups(self,event=None):
"""Update the listbox showing the groups for the selected calculation"""
#
# Add the groups to the listbox
#
self.group_disp.delete(0, END)
for group in self.groups:
self.group_disp.insert(END,group)
return | Update the listbox showing the groups for the selected calculation | Update the listbox showing the groups for the selected calculation | [
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] | def update_all_groups(self,event=None):
Add the groups to the listbox
self.group_disp.delete(0, END)
for group in self.groups:
self.group_disp.insert(END,group)
return | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | update_selected_calc | <not_specific> | def update_selected_calc(self,event=None):
"""Update the set of pKa values we're working with"""
#
# First store the selected groups from the old selection
#
if self.current_selected_calc:
self.calcs[self.current_selected_calc]['selected_groups']=self.selected_groups[... | Update the set of pKa values we're working with | Update the set of pKa values we're working with | [
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] | def update_selected_calc(self,event=None):
First store the selected groups from the old selection
if self.current_selected_calc:
self.calcs[self.current_selected_calc]['selected_groups']=self.selected_groups[:]
Then load the new stuff
new_calc=self.calc_select.get()
... | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | select_all | <not_specific> | def select_all(self,event=None):
"""Select all groups in the window"""
count=0
for group in self.groups:
self.group_disp.selection_set(count)
count=count+1
return | Select all groups in the window | Select all groups in the window | [
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] | def select_all(self,event=None):
count=0
for group in self.groups:
self.group_disp.selection_set(count)
count=count+1
return | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | select_group | <not_specific> | def select_group(self):
"""Transfer the selected group to the 'selected' window"""
for sel in self.group_disp.curselection():
group_num=int(sel)
sel_group=self.groups[group_num]
if not sel_group in self.selected_groups:
self.selected_groups.append(sel_... | Transfer the selected group to the 'selected' window | Transfer the selected group to the 'selected' window | [
"Transfer",
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"the",
"'",
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] | def select_group(self):
for sel in self.group_disp.curselection():
group_num=int(sel)
sel_group=self.groups[group_num]
if not sel_group in self.selected_groups:
self.selected_groups.append(sel_group)
self.update_selected_groups()
return | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | select_irregular_titcurvs | <not_specific> | def select_irregular_titcurvs(self):
"""Select irregular titration curves based on a fit to the Henderson-Hasselbalch equation"""
self.selected_groups=[]
import pKarun.pKa_general
X=pKarun.pKa_general.pKanalyse()
for group in self.groups:
#
# Include only ... | Select irregular titration curves based on a fit to the Henderson-Hasselbalch equation | Select irregular titration curves based on a fit to the Henderson-Hasselbalch equation | [
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] | def select_irregular_titcurvs(self):
self.selected_groups=[]
import pKarun.pKa_general
X=pKarun.pKa_general.pKanalyse()
for group in self.groups:
Include only groups with a pKa value
if self.pkavals[group]['pKa']:
solution,sq=X.fit_to_henderson(se... | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | display_details_sel | <not_specific> | def display_details_sel(self,event=None):
"""Display the details of the groups clicked in the selected window"""
self.details.delete(1.0, END)
#
# Loop over all groups
#
for sel in self.selected.curselection():
group_num=int(sel)
group=self.selecte... | Display the details of the groups clicked in the selected window | Display the details of the groups clicked in the selected window | [
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] | def display_details_sel(self,event=None):
self.details.delete(1.0, END)
Loop over all groups
for sel in self.selected.curselection():
group_num=int(sel)
group=self.selected_groups[group_num]
self.add_group_to_details(group)
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | display_details | <not_specific> | def display_details(self,event=None):
"""Display the details of the groups clicked in the list of all groups"""
#
# Do the details
#
self.details.delete(1.0, END)
#
# Loop over all groups
#
for sel in self.group_disp.curselection():
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Do the details
self.details.delete(1.0, END)
Loop over all groups
for sel in self.group_disp.curselection():
group_num=int(sel)
group=self.groups[group_num]
self.add_group_to_details(group)
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | add_group_to_details | <not_specific> | def add_group_to_details(self,group):
"""Add the details of a single group to the details window"""
X=pKarun.pKa_general.pKanalyse()
order=['modelpK','desolv','backgr','intpKa','delec','dpKa','pKa']
unit_dict={'modelpK':'','desolv':'pKa units','backgr':'pKa units','delec':'pKa units','dp... | Add the details of a single group to the details window | Add the details of a single group to the details window | [
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] | def add_group_to_details(self,group):
X=pKarun.pKa_general.pKanalyse()
order=['modelpK','desolv','backgr','intpKa','delec','dpKa','pKa']
unit_dict={'modelpK':'','desolv':'pKa units','backgr':'pKa units','delec':'pKa units','dpKa':'pKa units','pKa':'','intpKa':''}
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | show_matrix_table | <not_specific> | def show_matrix_table(self,event=None):
"""Open a new window with the matrix for all selected groups"""
details_win=Toplevel()
import pKarun.pKa_general
X=pKarun.pKa_general.pKanalyse()
row=0
order=sorted(self.matrix.keys())
#
# Insert table headings
... | Open a new window with the matrix for all selected groups | Open a new window with the matrix for all selected groups | [
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details_win=Toplevel()
import pKarun.pKa_general
X=pKarun.pKa_general.pKanalyse()
row=0
order=sorted(self.matrix.keys())
Insert table headings
column=0
for key in ['dpKa units']+order:
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | show_details_table | <not_specific> | def show_details_table(self,event=None):
"""Open a new window with all details for the groups selected"""
details_win=Toplevel()
import pKarun.pKa_general
X=pKarun.pKa_general.pKanalyse()
row=0
order=['Group','modelpK','desolv','backgr','intpKa','delec','dpKa','pKa','HH f... | Open a new window with all details for the groups selected | Open a new window with all details for the groups selected | [
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] | def show_details_table(self,event=None):
details_win=Toplevel()
import pKarun.pKa_general
X=pKarun.pKa_general.pKanalyse()
row=0
order=['Group','modelpK','desolv','backgr','intpKa','delec','dpKa','pKa','HH fit','HH fit pKa']
Insert table headings
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | update_selected_groups | <not_specific> | def update_selected_groups(self):
"""Update the display in the main window - both the list of groups, and the drawing of titration curves"""
#
# Sort
#
self.selected_groups.sort()
self.selected.delete(0, END)
for group in self.selected_groups:
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Sort
self.selected_groups.sort()
self.selected.delete(0, END)
for group in self.selected_groups:
self.selected.insert(END,group)
Copy it to the master array
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | model_rest_of_protein | <not_specific> | def model_rest_of_protein(self,model,set_pH):
"""Compile the information for modelling the rest of teh protein
model 0 = ignore
model 1 = non-titrating point charges (select charge at pH 7.0)
model 2 = fixed titrating charges
"""
wait_win=Toplevel()
self.set_geome... | Compile the information for modelling the rest of teh protein
model 0 = ignore
model 1 = non-titrating point charges (select charge at pH 7.0)
model 2 = fixed titrating charges
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self.set_geometry(self.master,wait_win)
wait_win.title('Please wait')
Label(wait_win,text='Calculating cumulated effect of all other groups').grid(row=0,column=0)
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | goto_pKa_system | <not_specific> | def goto_pKa_system(self):
"""Open dialog asking for how many groups"""
import tkSimpleDialog
num_groups=tkSimpleDialog.askinteger("Number of groups","Please enter number of titratable groups",
parent=self.master)
S=pKa_system.pKa_system(num_g... | Open dialog asking for how many groups | Open dialog asking for how many groups | [
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] | def goto_pKa_system(self):
import tkSimpleDialog
num_groups=tkSimpleDialog.askinteger("Number of groups","Please enter number of titratable groups",
parent=self.master)
S=pKa_system.pKa_system(num_groups,self.master)
return | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | select_strongly_interacting_groups | <not_specific> | def select_strongly_interacting_groups(self):
"""Select groups that interact strongly with the selected groups"""
self.matrix=self.X.read_matrix()
append_groups={}
#
# Loop over all selected groups and check for interaction energies
#
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self.matrix=self.X.read_matrix()
append_groups={}
Loop over all selected groups and check for interaction energies
interaction_energy_cutoff=self.int_cutoff.get()
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | load_titration | <not_specific> | def load_titration(self,pdbfilename=None):
"""Load the results of a pKa calculation"""
import os
if not pdbfilename:
pdbfilename=tkFileDialog.askopenfilename(defaultextension='.pdb',
initialdir=os.getcwd(),
... | Load the results of a pKa calculation | Load the results of a pKa calculation | [
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import os
if not pdbfilename:
pdbfilename=tkFileDialog.askopenfilename(defaultextension='.pdb',
initialdir=os.getcwd(),
filetypes=[("WHAT IF pK... | [
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | save_titration | <not_specific> | def save_titration(self):
"""Save all titrations in a pickled file"""
import tkFileDialog, os, pickle
savedir=os.getcwd()
filename=tkFileDialog.asksaveasfilename(defaultextension=".ppc",
initialfile='calculation1.ppc',
... | Save all titrations in a pickled file | Save all titrations in a pickled file | [
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import tkFileDialog, os, pickle
savedir=os.getcwd()
filename=tkFileDialog.asksaveasfilename(defaultextension=".ppc",
initialfile='calculation1.ppc',
initialdir=savedir,
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b37bde73a40919c61d69bb150590b71dff8b0ed9 | shambo001/peat | pKaTool/pKaTool_main.py | [
"MIT"
] | Python | subtract_titration | <not_specific> | def subtract_titration(self):
"""Subtract the second pKa calculation from the first to find differences in titration curves"""
#
# Choose the calc to subtract from
#
self.choose_win=Toplevel()
lbl=Label(self.choose_win,text='Which calculation should we subtract from %s' %... | Subtract the second pKa calculation from the first to find differences in titration curves | Subtract the second pKa calculation from the first to find differences in titration curves | [
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Choose the calc to subtract from
self.choose_win=Toplevel()
lbl=Label(self.choose_win,text='Which calculation should we subtract from %s' %self.calc_select.get())
lbl.grid(row=0,column=0,columnspan=4)
self.sub_calc=StringVar()
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a75dd86c86dfca6d2cd0d66fab3036fdc3ceb053 | shambo001/peat | DataPipeline/Importer.py | [
"MIT"
] | Python | guessRowStart | <not_specific> | def guessRowStart(self, lines):
"""If rowstart is not specified in config, it might be non-zero"""
s = 0
for line in lines:
if not self.checkEmptyRow(line):
s+=1
else:
self.rowstart = s
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s = 0
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s+=1
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a75dd86c86dfca6d2cd0d66fab3036fdc3ceb053 | shambo001/peat | DataPipeline/Importer.py | [
"MIT"
] | Python | checkValue | <not_specific> | def checkValue(self, val, format=''):
"""Coerce a string to float if possible"""
#add code to handle commas in thousand separators
dec = self.decimalsymbol
if format != '':
return self.checkTime(val, format)
if dec == '.':
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dec = self.decimalsymbol
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return self.checkTime(val, format)
if dec == '.':
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return None
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a75dd86c86dfca6d2cd0d66fab3036fdc3ceb053 | shambo001/peat | DataPipeline/Importer.py | [
"MIT"
] | Python | checkTime | <not_specific> | def checkTime(self, val, timeformat):
"""Coerce to a datetime object and return a value in seconds
from some reference"""
try:
dt = datetime.datetime.strptime(val,timeformat)
return dt
except ValueError, e:
print e
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | enable_group_editing | <not_specific> | def enable_group_editing(self,event):
"""Enable editing of the properties of a group"""
group_num=int(self.LB_added_groups.curselection()[0])
selected_group=self.selected_groups[group_num][0]
#
#
def get_new_colour():
import tkColorChooser
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] | def enable_group_editing(self,event):
group_num=int(self.LB_added_groups.curselection()[0])
selected_group=self.selected_groups[group_num][0]
def get_new_colour():
import tkColorChooser
rgb,colorstring=tkColorChooser.askcolor(self.group_properties[selected_group]['colour'... | [
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | update_diel | <not_specific> | def update_diel(event=None):
"""Update teh dielectric constant for a calc"""
diel=self.diel_var.get()
self.group_properties[selected_group]['diel']=diel
self.update_EM_effect_prediction()
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diel=self.diel_var.get()
self.group_properties[selected_group]['diel']=diel
self.update_EM_effect_prediction()
return | [
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | load_pdb | <not_specific> | def load_pdb(self,filename=None):
"""Load a PDB file and build all the HNs"""
import tkFileDialog, os
if hasattr(self,'savedir'):
savedir=self.savedir
else:
savedir=os.getcwd()
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if hasattr(self,'savedir'):
savedir=self.savedir
else:
savedir=os.getcwd()
if not filename:
filename=tkFileDialog.askopenfilename(defaultextension="*.pdb",
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | def_titgrp | <not_specific> | def def_titgrp(self):
"""Define a titratable group
There are two steps
1. Define the position
2. Define the titrational behaviour
"""
self.seldef_win=Toplevel()
self.set_geometry(self.master,self.seldef_win)
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | select_titgrp_frompdb | <not_specific> | def select_titgrp_frompdb(self,window=None):
"""Select a titratable group from the PDB file"""
#
# We can do this in any window
#
if not window:
window=self.seldef_win
#
# Make the dialog
#
titgrps=self.PI.titratable_groups.keys()
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We can do this in any window
if not window:
window=self.seldef_win
Make the dialog
titgrps=self.PI.titratable_groups.keys()
titgrps.sort()
self.titgroups_inPDB=[]
for res in titgrps:
for titgrp... | [
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | update_EM_effect_prediction | <not_specific> | def update_EM_effect_prediction(self,do_yasara=None):
"""Recalculate all EM effects and redraw all"""
#
# Should we recolour yasara?
#
if self.yasara and do_yasara:
do_yasara=True
#
# First delete the bars from last time
#
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] | def update_EM_effect_prediction(self,do_yasara=None):
Should we recolour yasara?
if self.yasara and do_yasara:
do_yasara=True
First delete the bars from last time
if not hasattr(self,'graph_bars'):
self.graph_bars={}
for bar in self.graph_bars.keys():
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | print_chemshift_to_file | <not_specific> | def print_chemshift_to_file(self):
"""Print the chemical shift canvas to file"""
import sys, os
import tkFileDialog, os
if not hasattr(self,'lastdir'):
self.lastdir=os.getcwd()
filename=tkFileDialog.asksaveasfilename(defaultextension='.ps',
... | Print the chemical shift canvas to file | Print the chemical shift canvas to file | [
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import sys, os
import tkFileDialog, os
if not hasattr(self,'lastdir'):
self.lastdir=os.getcwd()
filename=tkFileDialog.asksaveasfilename(defaultextension='.ps',
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | load_csv | <not_specific> | def load_csv(self,filename=None,group=None):
"""Open a file with chem shift data"""
self.exp_group_selected=group
#
# Make sure we have the expdata array
#
if not hasattr(self,'expdata'):
self.expdata={}
#
# Load data
#
... | Open a file with chem shift data | Open a file with chem shift data | [
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self.exp_group_selected=group
Make sure we have the expdata array
if not hasattr(self,'expdata'):
self.expdata={}
Load data
import tkFileDialog, os
savedir=os.getcwd()
if not filename:
filename... | [
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c19178b82aed4697ad34f77c541ab11a0e83347d | shambo001/peat | Ghost/EM_effect.py | [
"MIT"
] | Python | load_full_titdata | <not_specific> | def load_full_titdata(self,filename=None,pH_start=5.2,pH_end=7.2):
"""Load a full set of titration data from en Ekin project file"""
import full_titfit
self.fullfit=full_titfit.titfitter(filename,pH_start,pH_end)
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import full_titfit
self.fullfit=full_titfit.titfitter(filename,pH_start,pH_end)
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | loadPrefs | <not_specific> | def loadPrefs(self):
"""Load prefs from a preferences instance"""
self.preferences = Preferences('DNATool2',{})
temp = {}
for key in self.defaultprefs:
if not key in self.preferences.prefs:
self.preferences.set(key, self.defaultprefs[key])
temp[key... | Load prefs from a preferences instance | Load prefs from a preferences instance | [
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] | def loadPrefs(self):
self.preferences = Preferences('DNATool2',{})
temp = {}
for key in self.defaultprefs:
if not key in self.preferences.prefs:
self.preferences.set(key, self.defaultprefs[key])
temp[key] = self.preferences.get(key)
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | savePrefs | <not_specific> | def savePrefs(self):
"""Save prefs to a preferences instance"""
self.applyPrefs(self.prefsdialog.getValues())
self.preferences = Preferences('DNATool2',{})
for key in self.defaultprefs:
self.preferences.set(key, self.__dict__[key])
return | Save prefs to a preferences instance | Save prefs to a preferences instance | [
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self.applyPrefs(self.prefsdialog.getValues())
self.preferences = Preferences('DNATool2',{})
for key in self.defaultprefs:
self.preferences.set(key, self.__dict__[key])
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | applyPrefs | <not_specific> | def applyPrefs(self, prefs=None):
"""Apply prefs from a given dict"""
if prefs == None: prefs=self.defaultprefs
for key in prefs:
self.__dict__[key] = prefs[key]
return | Apply prefs from a given dict | Apply prefs from a given dict | [
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] | def applyPrefs(self, prefs=None):
if prefs == None: prefs=self.defaultprefs
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self.__dict__[key] = prefs[key]
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | createMenuBar | <not_specific> | def createMenuBar(self):
"""Create the menu bar for the application. """
self.menu=Menu(self.main)
self.file_menu={'01Open Project':{'cmd':self.openProject},
'02Open Sequence':{'cmd':self.openSequence},
'05Quit':{'cmd':self.quit}}
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self.menu=Menu(self.main)
self.file_menu={'01Open Project':{'cmd':self.openProject},
'02Open Sequence':{'cmd':self.openSequence},
'05Quit':{'cmd':self.quit}}
self.file_menu=self.create_pulldown(self.menu,self.file_menu)
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | createSidePane | <not_specific> | def createSidePane(self, width=200):
"""Side panel for various dialogs is tabbed notebook that can hold multiple
dialogs at once """
self.closeSidePane()
self.sidepane = Frame(self.m,
bd=1,relief=RAISED)
self.sidepane = Pmw.NoteBook(self.m)
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] | def createSidePane(self, width=200):
self.closeSidePane()
self.sidepane = Frame(self.m,
bd=1,relief=RAISED)
self.sidepane = Pmw.NoteBook(self.m)
self.sidepane.component('hull').configure(relief='sunken',
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | createChildFrame | <not_specific> | def createChildFrame(self, sidepane=True, width=400, name=None):
"""Create a child frame in sidepane notebook or as toplevel"""
geometry = '600x400+500+250'
if sidepane == True:
cframe = self.sidepane.add(name)
self.sidepane.tab(name).configure(font='fixed 8',anchor='w')
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] | def createChildFrame(self, sidepane=True, width=400, name=None):
geometry = '600x400+500+250'
if sidepane == True:
cframe = self.sidepane.add(name)
self.sidepane.tab(name).configure(font='fixed 8',anchor='w')
self.sidepane.selectpage(name)
else:
cf... | [
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | detachChildFrame | <not_specific> | def detachChildFrame(self):
"""Since we cannot actually detach frames in Tkinter, we
remove the frame in the sidepane make a new toplevel window"""
name = self.sidepane.getcurselection()
self.sidepane.delete(name)
if name == 'PrimerDB':
fr = self.createPrimerDBGUI(... | Since we cannot actually detach frames in Tkinter, we
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name = self.sidepane.getcurselection()
self.sidepane.delete(name)
if name == 'PrimerDB':
fr = self.createPrimerDBGUI(sidepane=False)
else:
fr = self.createChildFrame(sidepane=False, name=name)
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | toggleApps | <not_specific> | def toggleApps(self, name):
"""Remove or add apps from view"""
print name
if self.appsvars[name].get() == 1:
if not hasattr(self, name):
fr = self.createChildFrame(sidepane=True, name=name)
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print name
if self.appsvars[name].get() == 1:
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fr = self.createChildFrame(sidepane=True, name=name)
else:
if hasattr(self, name):
if name in self.sidepane.pagenames():
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | tileHorizontal | <not_specific> | def tileHorizontal(self):
"""Re-arrange paned widgets horizontally"""
if self.orientation == 'horizontal':
return
self.removeAll()
self.orientation = 'horizontal'
self.setupGUI()
return | Re-arrange paned widgets horizontally | Re-arrange paned widgets horizontally | [
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self.removeAll()
self.orientation = 'horizontal'
self.setupGUI()
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | tileVertical | <not_specific> | def tileVertical(self):
"""Re-arrange paned widgets vertically"""
if self.orientation == 'vertical':
return
self.removeAll()
self.orientation = 'vertical'
self.setupGUI()
return | Re-arrange paned widgets vertically | Re-arrange paned widgets vertically | [
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0d2ef155cf1dbd8ac38122a02a610e5298878842 | shambo001/peat | DNATool2/DNAToolApp.py | [
"MIT"
] | Python | createPrimerDBGUI | <not_specific> | def createPrimerDBGUI(self, sidepane=True):
"""We create this individually to avoid confusion"""
if hasattr(self, 'PrimerDB'):
self.PrimerDB.lift()
return
fr = self.createChildFrame(name='PrimerDB',sidepane=sidepane)
self.pdbwin = PrimerDBGUI(fr, database=self.pri... | We create this individually to avoid confusion | We create this individually to avoid confusion | [
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if hasattr(self, 'PrimerDB'):
self.PrimerDB.lift()
return
fr = self.createChildFrame(name='PrimerDB',sidepane=sidepane)
self.pdbwin = PrimerDBGUI(fr, database=self.primerdb)
self.pdbwin.update()
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
"MIT"
] | Python | createMenuBar | <not_specific> | def createMenuBar(self):
"""Create the menu bar for the application. """
self.menu=Menu(self.mainwin)
self.file_menu={ '01Open Ekin project':{'cmd':self.loadEkinProj},
'02Open DB':{'cmd':self.openDB},
'03Quit':{'cmd':self.quit}}
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self.menu=Menu(self.mainwin)
self.file_menu={ '01Open Ekin project':{'cmd':self.loadEkinProj},
'02Open DB':{'cmd':self.openDB},
'03Quit':{'cmd':self.quit}}
self.file_menu=self.create_pulldown(self.menu,self.file_menu)
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
"MIT"
] | Python | selectfromDB | <not_specific> | def selectfromDB(self):
"""Get an ekin prj from the DB"""
if self.DB == None:
return
from PEATDB.Actions import DBActions
fr=Toplevel()
rbox, cbox = DBActions.getRecordsSelector(self.DB,fr)
def loadselected():
item = rbox.curselection()[0]
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if self.DB == None:
return
from PEATDB.Actions import DBActions
fr=Toplevel()
rbox, cbox = DBActions.getRecordsSelector(self.DB,fr)
def loadselected():
item = rbox.curselection()[0]
rec = self.DB.getRecs()[int(item)]
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
"MIT"
] | Python | showEkinTable | <not_specific> | def showEkinTable(self, parent, E=None):
"""Show a list of ekin prj datasets in a table"""
self.currentmodel = EkinProjModel(E)
fr=Frame(parent)
self.pw.add(fr,minsize=200)
self.ekintable = EkinProjTable(fr, self.currentmodel)
self.ekintable.createTableFrame()
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self.currentmodel = EkinProjModel(E)
fr=Frame(parent)
self.pw.add(fr,minsize=200)
self.ekintable = EkinProjTable(fr, self.currentmodel)
self.ekintable.createTableFrame()
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
"MIT"
] | Python | analysepKas | <not_specific> | def analysepKas(self, p=None):
"""Get the main pKas of all/titr group and do analysis"""
E = self.currprj
if E==None: return
t = TitrationAnalyser()
if p == None:
p = t.findpKas(E, titratable=True, reliable=False, minspan=0.06)
t.analysepKas(p)
return | Get the main pKas of all/titr group and do analysis | Get the main pKas of all/titr group and do analysis | [
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E = self.currprj
if E==None: return
t = TitrationAnalyser()
if p == None:
p = t.findpKas(E, titratable=True, reliable=False, minspan=0.06)
t.analysepKas(p)
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
"MIT"
] | Python | titDBUtils | <not_specific> | def titDBUtils(self, DB=None, col=None, prot=None, a=None, E=None,
refit=False, addmeta=False, getexperrs=False,
yuncert=None):
"""Add some meta and refit all for an ekin prj or a rec/field in db"""
if E==None and DB != None:
E = DB[prot][col]
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if E==None and DB != None:
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E.checkDatasets()
t = TitrationAnalyser()
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
"MIT"
] | Python | benchmarkExpErr | <not_specific> | def benchmarkExpErr(self, DB):
"""Test effects of model and noise on est exp error technique"""
E = DB['HEWL']['1H NMR']
d='D66N-HN'
E.plotDatasets(d,filename='experrtest.png')
print E.getFitData(d)
ferrs = E.estimateExpUncertainty(d, runs=20,
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E = DB['HEWL']['1H NMR']
d='D66N-HN'
E.plotDatasets(d,filename='experrtest.png')
print E.getFitData(d)
ferrs = E.estimateExpUncertainty(d, runs=20,
xuncert=0.1, yuncert=0.03)
print ferrs
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d2c16c3cc5d636f9743c2e2b0b87f18e4375fcea | shambo001/peat | PEATDB/plugins/titranalysis.py | [
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] | Python | addpKaTables | <not_specific> | def addpKaTables(self, DB, names, col='1H NMR'):
"""Create labbook tables for 'real' pKas for required proteins"""
t = TitrationAnalyser()
prots = t.getProtNames(DB)
for name in names:
recname = DB.getRecordName(name)
E = DB[recname][col]
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t = TitrationAnalyser()
prots = t.getProtNames(DB)
for name in names:
recname = DB.getRecordName(name)
E = DB[recname][col]
titrresidues = t.getResidues(E, titratable=True)
S = DB.createLabbookSheet(... | [
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abd81230ee2d4ee092100b179d86320e78d7d53f | shambo001/peat | PEATDB/plugins/Summary.py | [
"MIT"
] | Python | populate | <not_specific> | def populate(self):
"""Clear the current data and populate with db data
from dbs in projects dictionary"""
print self.DB
if self.DB == None:
return
for db in self.projects:
recs = db.getRecs() | Clear the current data and populate with db data
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print self.DB
if self.DB == None:
return
for db in self.projects:
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caaf0b255f1c38b405dfbe102920360f68120f16 | shambo001/peat | Protool/Yasara_interface.py | [
"MIT"
] | Python | shortMD | <not_specific> | def shortMD(self,pdblines):
"""Do a short MD in vacou to get an ensemble"""
objs=self.Y.BuildPDB(pdblines)
self.Y.DelRes('WAT')
self.Y.DelRes('HOH')
self.Y.Clean()
self.Y.CellAuto(extension=10)
self.Y.ForceField('Amber99')
self.Y.Boundary('Periodic')
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self.Y.DelRes('WAT')
self.Y.DelRes('HOH')
self.Y.Clean()
self.Y.CellAuto(extension=10)
self.Y.ForceField('Amber99')
self.Y.Boundary('Periodic')
self.Y.TempCtrl('SteepDes')
self.Y.Sim('On')
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3e47e3408abebefc99058533e086f4ade8ad3af6 | shambo001/peat | pKaTool/Ghosts/Chemical_shift_md.py | [
"MIT"
] | Python | parseCharges | <not_specific> | def parseCharges(self):
'''
Parse charges from the topology file
'''
try:
fd = open(self.top, 'r');
lines = fd.readlines()
fd.close()
except IOError:
print '\n\t\tFATAL: Cannot open %s file'%self.top
sys.exit(1)
chargeDict = {}
for lineNum in range(len(lines)):
if lines[lineNum].strip() ... |
Parse charges from the topology file
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try:
fd = open(self.top, 'r');
lines = fd.readlines()
fd.close()
except IOError:
print '\n\t\tFATAL: Cannot open %s file'%self.top
sys.exit(1)
chargeDict = {}
for lineNum in range(len(lines)):
if lines[lineNum].strip() == '[ atoms ]':
for lineNum1 in range(lineNum+2... | [
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3e47e3408abebefc99058533e086f4ade8ad3af6 | shambo001/peat | pKaTool/Ghosts/Chemical_shift_md.py | [
"MIT"
] | Python | parseCoord | <not_specific> | def parseCoord(self, pdb):
'''
Parse coordinates from the pdb file
'''
try:
fd = open(pdb, 'r');
lines = fd.readlines()
fd.close()
except:
print '\n\t\tFATAL: Cannot open %s file'%pdb
sys.exit(1)
coordMol = {}
coordSol = {}
coordCl = {}
for line in lines:
record = line[:6].strip(... |
Parse coordinates from the pdb file
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try:
fd = open(pdb, 'r');
lines = fd.readlines()
fd.close()
except:
print '\n\t\tFATAL: Cannot open %s file'%pdb
sys.exit(1)
coordMol = {}
coordSol = {}
coordCl = {}
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
resNum = parseResNum(lin... | [
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3e47e3408abebefc99058533e086f4ade8ad3af6 | shambo001/peat | pKaTool/Ghosts/Chemical_shift_md.py | [
"MIT"
] | Python | calculateCSP | <not_specific> | def calculateCSP(self):
'''
calculates potentials of all N, C (N and H) atoms from num1 and num2 side chains, protein, water and Cl
'''
fd_progress = open("progress.log", 'a');
fileFirst = self.pdb + '.pdb.' + str(self.start)
coordMol, coordSol, coordCl = self.parseCoord(fileFirst)
resNumsMol = coordMo... |
calculates potentials of all N, C (N and H) atoms from num1 and num2 side chains, protein, water and Cl
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fd_progress = open("progress.log", 'a');
fileFirst = self.pdb + '.pdb.' + str(self.start)
coordMol, coordSol, coordCl = self.parseCoord(fileFirst)
resNumsMol = coordMol.keys()
resNumsMol.sort()
resNumsSol = coordSol.keys()
resNumsSol.sort()
resNumsCl = coordCl.keys()
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3e47e3408abebefc99058533e086f4ade8ad3af6 | shambo001/peat | pKaTool/Ghosts/Chemical_shift_md.py | [
"MIT"
] | Python | plot | null | def plot(self):
'''
Plot the outcome of the MD simulations
'''
import matplotlib
matplotlib.use('Agg')
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from matplotlib import cm
import numpy as np
fileFirst = self.pdb + '.pdb.' + str(self.start)
coordMol, coordSol, coordC... |
Plot the outcome of the MD simulations
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import matplotlib
matplotlib.use('Agg')
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
from matplotlib import cm
import numpy as np
fileFirst = self.pdb + '.pdb.' + str(self.start)
coordMol, coordSol, coordCl = self.parseCoord(fileFirst)
resNumsMol = coordMol.k... | [
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b8840143c56d36dc7944c001646d41a0066171e4 | shambo001/peat | PEATDB/DNAtool/DNA_sequencing.py | [
"MIT"
] | Python | show_DNAseq | <not_specific> | def show_DNAseq(self,seqfile=None,usecurrent=0,clearprev=1,level=0):
"""Load and display a sequence from a file"""
if seqfile==None:
seqfile = self.main_self.dnaseq_read(newprotein=None,variable='seq_comp',var2='seq_comp_file')
# Pass the file to dnaseq_read instead of getting it to... | Load and display a sequence from a file | Load and display a sequence from a file | [
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if seqfile==None:
seqfile = self.main_self.dnaseq_read(newprotein=None,variable='seq_comp',var2='seq_comp_file')
else:
self.main_self.dnaseq_read(newprotein=None,fileinput=seqfile,variable='seq_comp',
... | [
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b8840143c56d36dc7944c001646d41a0066171e4 | shambo001/peat | PEATDB/DNAtool/DNA_sequencing.py | [
"MIT"
] | Python | show_multiple_DNAseq_dialog | <not_specific> | def show_multiple_DNAseq_dialog(self):
"""
This function provides a dialog to view and select the multiple loaded sequences
"""
self.choose_seq_win=Toplevel()
self.choose_seq_win.title("Load Multiple DNA Sequences")
#self.choose_seq_win.geometry("%dx%d%+d%+d" % (40, 20, 0... |
This function provides a dialog to view and select the multiple loaded sequences
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] | def show_multiple_DNAseq_dialog(self):
self.choose_seq_win=Toplevel()
self.choose_seq_win.title("Load Multiple DNA Sequences")
self.choose_seq_win.geometry("+%d+%d" % (self.parent.master_win.winfo_rootx()+550,
self.parent.master_win.winfo_rooty()+100))
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b8840143c56d36dc7944c001646d41a0066171e4 | shambo001/peat | PEATDB/DNAtool/DNA_sequencing.py | [
"MIT"
] | Python | load_multiple | <not_specific> | def load_multiple(self,event=None):
"""load multiple files and show them in the details widget"""
# a list with the current sequences loaded for display
self.seq_list=[]
self.seq_list_direction={}
self.clear_list()
# populate file list here
self.seq_list = self.op... | load multiple files and show them in the details widget | load multiple files and show them in the details widget | [
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] | def load_multiple(self,event=None):
self.seq_list=[]
self.seq_list_direction={}
self.clear_list()
self.seq_list = self.open_filelist()
for name in self.seq_list:
x = os.path.split(name)
self.details.insert(END,x[1])
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b8840143c56d36dc7944c001646d41a0066171e4 | shambo001/peat | PEATDB/DNAtool/DNA_sequencing.py | [
"MIT"
] | Python | display_current | null | def display_current(self,event=None):
"""Display the current sequences selected in the listbox"""
# Reset this if main window has been cleared while listbox open
self.main_self.show_comp_sequence.set(1)
self.main_self.maxseqlevel=0
self.main_self.seqframe.delete('strip')
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self.main_self.show_comp_sequence.set(1)
self.main_self.maxseqlevel=0
self.main_self.seqframe.delete('strip')
tmp_sel = map(int, self.details.curselection())
p=0
if len(tmp_sel)==1:
num=tmp_sel[0]
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b8840143c56d36dc7944c001646d41a0066171e4 | shambo001/peat | PEATDB/DNAtool/DNA_sequencing.py | [
"MIT"
] | Python | change_seq_direction | <not_specific> | def change_seq_direction(self,event=None):
"""Sets forward or reverse sense for entry based on single/double-click"""
#pop up dialog box here first time this entry is selected
#sel=self.details.curselection()
items = map(int, self.details.curselection())
num=items[0]
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items = map(int, self.details.curselection())
num=items[0]
name=self.seq_list[num]
if self.seq_list_direction[name]=='f':
self.details.itemconfig(num,fg='red')
self.seq_list_direction[name]=='r'
else:
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b8840143c56d36dc7944c001646d41a0066171e4 | shambo001/peat | PEATDB/DNAtool/DNA_sequencing.py | [
"MIT"
] | Python | load_Zip | <not_specific> | def load_Zip(self,event=None):
"""Loads sequences from a zip file and show items in the details widget"""
zfilename = None
zfilename = self.open_zipfile()
if zfilename == None:
return
zfile = zipfile.ZipFile( zfilename, "r" )
zfile.printdir()
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zfilename = None
zfilename = self.open_zipfile()
if zfilename == None:
return
zfile = zipfile.ZipFile( zfilename, "r" )
zfile.printdir()
self.seq_list=[]
for info in zfile.infolist():
fname = info.filename
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70c95c080e7643064aab176f3d6c440bd1816f44 | shambo001/peat | pKa/get_muts.py | [
"MIT"
] | Python | main | <not_specific> | def main(options,args):
"""Extract mutations from a multiple sequence alignment"""
import PEATDB.sequence_alignment as SA
if not options.fasta:
alignment=SA.read_clustal_aln_file(args[0])
else:
alignment=SA.read_fasta_aln_file(args[0])
print sorted(alignment.keys())
HEWL_seq=ali... | Extract mutations from a multiple sequence alignment | Extract mutations from a multiple sequence alignment | [
"Extract",
"mutations",
"from",
"a",
"multiple",
"sequence",
"alignment"
] | def main(options,args):
import PEATDB.sequence_alignment as SA
if not options.fasta:
alignment=SA.read_clustal_aln_file(args[0])
else:
alignment=SA.read_fasta_aln_file(args[0])
print sorted(alignment.keys())
HEWL_seq=alignment[options.wt]
fd=open('mutations.txt','w')
fd2=open... | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | Timeit | <not_specific> | def Timeit(func,number=1,module="__main__"):
""" A wrapper which can be used to time any function """
name = func.__name__
t = timeit.Timer("%s()"%name, "from %s import %s" % (module, name))
return "%.2f usec/pass" % (1000000*t.timeit(number=number)/number) | A wrapper which can be used to time any function | A wrapper which can be used to time any function | [
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] | def Timeit(func,number=1,module="__main__"):
name = func.__name__
t = timeit.Timer("%s()"%name, "from %s import %s" % (module, name))
return "%.2f usec/pass" % (1000000*t.timeit(number=number)/number) | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | createdb | <not_specific> | def createdb(local=None, server=None, project=None, username=None, norecs=1000):
"""Create and add some test data"""
if local != None:
if os.path.exists(local):
for i in ['.lock','.index','']:
try:
os.remove(local+i)
except:
... | Create and add some test data | Create and add some test data | [
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"some",
"test",
"data"
] | def createdb(local=None, server=None, project=None, username=None, norecs=1000):
if local != None:
if os.path.exists(local):
for i in ['.lock','.index','']:
try:
os.remove(local+i)
except:
pass
DB = PDatabase(local=l... | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | checkdb | <not_specific> | def checkdb(server=None, project=None, local=None):
"""test basic ops for the db"""
if server != None:
DB = PDatabase(server=server, port=8080,
username='farrell',
password='123',
project=project)
else:
DB = PDatabase(local=local)
pr... | test basic ops for the db | test basic ops for the db | [
"test",
"basic",
"ops",
"for",
"the",
"db"
] | def checkdb(server=None, project=None, local=None):
if server != None:
DB = PDatabase(server=server, port=8080,
username='farrell',
password='123',
project=project)
else:
DB = PDatabase(local=local)
print DB
print DB['userfields']
... | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | testBlob | <not_specific> | def testBlob():
"""write a file as binary data to blob and read back"""
from ZODB.PersistentMapping import PersistentMapping
import mimetypes
from PILView import PILViewer
DB = PDatabase(server='localhost',port=8090,
username='farrell',
password='123')
def addfile(... | write a file as binary data to blob and read back | write a file as binary data to blob and read back | [
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] | def testBlob():
from ZODB.PersistentMapping import PersistentMapping
import mimetypes
from PILView import PILViewer
DB = PDatabase(server='localhost',port=8090,
username='farrell',
password='123')
def addfile(fname):
myblob = Blob()
b=myblob.open('w')
... | [
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"outlier_params": [],
"others": []
} |
b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | testLoading | <not_specific> | def testLoading():
"""Test loading times for large DB"""
from PEATDB.PEATTables import PEATTableModel
t1 = time()
DB = PDatabase(local='large.fs')
#DB = PDatabase(server='localhost', port=8080, username='farrell',
# password='123', project='large')
t2=time()
pr... | Test loading times for large DB | Test loading times for large DB | [
"Test",
"loading",
"times",
"for",
"large",
"DB"
] | def testLoading():
from PEATDB.PEATTables import PEATTableModel
t1 = time()
DB = PDatabase(local='large.fs')
t2=time()
print round(t2 - t1,2)
print DB.getRecs()
t3=time()
print round(t3 - t2,2)
print DB.meta
t4=time()
print t4 - t3
M = PEATTableModel(DB)
print M
t... | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | testMemory | <not_specific> | def testMemory():
"""test memory behaviour of DB, how can cache be managed"""
DB = PDatabase(server='localhost', username='farrell',
password='123', project='novo')
#DB = PDatabase(local='large.fs')
print DB
db = DB.db
print db.cacheSize()
for k in DB.getRecs()[:50]... | test memory behaviour of DB, how can cache be managed | test memory behaviour of DB, how can cache be managed | [
"test",
"memory",
"behaviour",
"of",
"DB",
"how",
"can",
"cache",
"be",
"managed"
] | def testMemory():
DB = PDatabase(server='localhost', username='farrell',
password='123', project='novo')
print DB
db = DB.db
print db.cacheSize()
for k in DB.getRecs()[:50]:
r=DB[k]
r.name
if db.cacheSize()>500:
db.cacheMinimize()
prin... | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | convertClass | <not_specific> | def convertClass():
"""Convert records to proper module name"""
project='test'
DB=PDatabase(server='localhost',port=8080,
username='farrell',password='123',
project=project)
for k in DB.getRecs():
r=PEATRecord(k)
rec = DB.data[k]
print rec.__cl... | Convert records to proper module name | Convert records to proper module name | [
"Convert",
"records",
"to",
"proper",
"module",
"name"
] | def convertClass():
project='test'
DB=PDatabase(server='localhost',port=8080,
username='farrell',password='123',
project=project)
for k in DB.getRecs():
r=PEATRecord(k)
rec = DB.data[k]
print rec.__class__
for f in rec.getFields():
... | [
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b9d89dcef3eba497e0964f68844e35354311170d | shambo001/peat | PEATDB/zodbtest.py | [
"MIT"
] | Python | convertEkinprjs | <not_specific> | def convertEkinprjs(local=None, server=None,
project=None, username=None):
"""convert old ekin prjs in a db to new"""
if local != None:
DB = PDatabase(local=local)
elif server != None:
DB = PDatabase(server=server, username='farrell', port=8080,
... | convert old ekin prjs in a db to new | convert old ekin prjs in a db to new | [
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] | def convertEkinprjs(local=None, server=None,
project=None, username=None):
if local != None:
DB = PDatabase(local=local)
elif server != None:
DB = PDatabase(server=server, username='farrell', port=8080,
password='123', project=project)
for f in D... | [
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"docstring_tokens"... |
a3c82e3761662550d6551c78f3a376c94689caec | shambo001/peat | pKa/Design_pKa.py | [
"MIT"
] | Python | calculate_pKa_change | <not_specific> | def calculate_pKa_change(self,mutations):
""" Calculate the dpKa value(s) for the residue(s) in self.desired_pKa_changes
and calculate the score for this set of mutations"""
#
# Which method are we going to use?
#
dpKas=None
if not self.params['tabulated']:
... | Calculate the dpKa value(s) for the residue(s) in self.desired_pKa_changes
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Which method are we going to use?
dpKas=None
if not self.params['tabulated']:
Explicit (each combination of mutations is evaluated separately)
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a3c82e3761662550d6551c78f3a376c94689caec | shambo001/peat | pKa/Design_pKa.py | [
"MIT"
] | Python | find_reporter_groups | <not_specific> | def find_reporter_groups(self,mutations,check_groups=False):
"""Find all the reporter groups that are valid with this set of mutations
If check_groups is True then check that the pKa values of the groups are
inside pH_start and pH_stop
"""
if not check_groups:
repor... | Find all the reporter groups that are valid with this set of mutations
If check_groups is True then check that the pKa values of the groups are
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if not check_groups:
reporter_groups=self.desired_pKa_changes.keys()
else:
If so requested get dpKa values for all wild type residues
reporter_groups=[]
groups=self.wt_pKas.keys()
gr... | [
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If check_groups is True then check that the pKa values of the groups are
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a3c82e3761662550d6551c78f3a376c94689caec | shambo001/peat | pKa/Design_pKa.py | [
"MIT"
] | Python | dpKa_philn10 | <not_specific> | def dpKa_philn10(self,mutation,target_residue,verbose=None):
"""
# For a given mutation, calculate the change in the pKa value if the target using phi/ln(10)
"""
# If we have no mutation, then we have no change
#
if not mutation:
return 0.0
#
#... |
# For a given mutation, calculate the change in the pKa value if the target using phi/ln(10)
| For a given mutation, calculate the change in the pKa value if the target using phi/ln(10) | [
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if not mutation:
return 0.0
Check that target_residue and mutation is not the same residue
import pKD_tools
if pKD_tools.get_resnum_from_mut(mutation)==pKD_tools.get_resnum_from_res(target_residue):
ret... | [
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"docstring_tokens... |
a3c82e3761662550d6551c78f3a376c94689caec | shambo001/peat | pKa/Design_pKa.py | [
"MIT"
] | Python | calc_dpKa | <not_specific> | def calc_dpKa(self):
"""
# Calculate the dpKa for a particular set of mutations
"""
# Initialise
#
self.initialise('calcdpka')
#
# Calculate starting state (wt pKa vals)
#
none_muts=[None]
#
# Set the mutations
#
... |
# Calculate the dpKa for a particular set of mutations
| Calculate the dpKa for a particular set of mutations | [
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] | def calc_dpKa(self):
self.initialise('calcdpka')
Calculate starting state (wt pKa vals)
none_muts=[None]
Set the mutations
mutations=self.params['mutations']
if not mutations:
self.O._print('You have to specify mutations with the -mutations flag when calcula... | [
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],
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} |
a3c82e3761662550d6551c78f3a376c94689caec | shambo001/peat | pKa/Design_pKa.py | [
"MIT"
] | Python | close_stdout | <not_specific> | def close_stdout(self):
"""Closes std out and dumps output to file"""
import tempfile, sys
self.newstdout=tempfile.TemporaryFile()
self.old_stdout=sys.stdout
sys.stdout=self.newstdout
return | Closes std out and dumps output to file | Closes std out and dumps output to file | [
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"file"
] | def close_stdout(self):
import tempfile, sys
self.newstdout=tempfile.TemporaryFile()
self.old_stdout=sys.stdout
sys.stdout=self.newstdout
return | [
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} |
a3c82e3761662550d6551c78f3a376c94689caec | shambo001/peat | pKa/Design_pKa.py | [
"MIT"
] | Python | run_opt | <not_specific> | def run_opt(defaults,new_instance=None,mutant_PDB_files={}):
"""
Do post-processing of defaults and branch into correct routine
"""
#
# Did we get a new design instance?
#
global G_Design_instance
if new_instance:
G_Design_instance=None
#
# Reformat parameters first thoug... |
Do post-processing of defaults and branch into correct routine
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Did we get a new design instance?
global G_Design_instance
if new_instance:
G_Design_instance=None
Reformat parameters first though...
params={}
for key in defaults.keys():
params[key]=defaults[key][0]
Print setu... | [
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71f14c6afddd3e5ecb26462c06a6011f9100d114 | shambo001/peat | DNATool2/Base.py | [
"MIT"
] | Python | savePrefs | <not_specific> | def savePrefs(self):
"""Save prefs to a preferences instance"""
self.preferences = Preferences('DNATool2',{})
for key in self.defaultprefs:
self.preferences.set(key, self.__dict__[key])
return | Save prefs to a preferences instance | Save prefs to a preferences instance | [
"Save",
"prefs",
"to",
"a",
"preferences",
"instance"
] | def savePrefs(self):
self.preferences = Preferences('DNATool2',{})
for key in self.defaultprefs:
self.preferences.set(key, self.__dict__[key])
return | [
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} |
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