omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Added --titrate_only option and tests for it.

Browse Source 
This option makes it possible for PROPKA to treat only a subset of protein
residues as titratable.
This commit is contained in:
Matvey Adzhigirey
2014-08-13 11:13:55 -07:00
committed by Mike Beachy
parent c420b4c2a5
commit 8084b31393
5 changed files with 112 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

46
propka/conformation_container.py
View File

@@ -31,11 +31,13 @@ class Conformation_container:
for atom in self.get_non_hydrogen_atoms():
# has this atom been checked for groups?
if atom.groups_extracted == 0:
self.validate_group(propka.group.is_group(self.parameters, atom))
# if the atom has been checked in a another conformation, check if it has a
# group that should be used in this conformation as well
elif atom.group:
self.validate_group(atom.group)
group = propka.group.is_group(self.parameters, atom)
else:
group = atom.group
# if the atom has been checked in a another conformation, check if it has a
# group that should be used in this conformation as well
if group:
self.setup_and_add_group(group)
return
@@ -130,8 +132,9 @@ class Conformation_container:
return res
def validate_group(self, group):
def setup_and_add_group(self, group):
""" Checks if we want to include this group in the calculations """
# Is it recognized as a group at all?
if not group:
return
@@ -139,18 +142,25 @@ class Conformation_container:
# Other checks (include ligands, which chains etc.)
# if all ok, accept the group
self.accept_group(group)
return
self.init_group(group)
self.groups.append(group)
def accept_group(self, group):
def init_group(self, group):
"""
Initialize the given Group object.
"""
# set up the group
group.parameters=self.parameters
group.setup()
# and store it
self.groups.append(group)
return
# If --titrate_only option is set, make non-specified residues un-titratable:
titrate_only = self.molecular_container.options.titrate_only
if titrate_only is not None:
at = group.atom
if not (at.chainID, at.resNumb, at.icode) in titrate_only:
group.titratable = False
if group.residue_type == 'CYS':
group.exclude_cys_from_results = True
#
@@ -334,8 +344,14 @@ class Conformation_container:
def get_titratable_groups(self):
return [group for group in self.groups if group.titratable]
def get_titratable_groups_and_cysteine_bridges(self):
return [group for group in self.groups if group.titratable or group.residue_type == 'CYS']
def get_groups_for_calculations(self):
"""
Returns a list of groups that should be included in results report.
If --titrate_only option is specified, only residues that are titratable
and are in that list are included; otherwise all titratable residues
and CYS residues are included.
"""
return [group for group in self.groups if group.use_in_calculations()]
def get_acids(self):
return [group for group in self.groups if (group.residue_type in self.parameters.acid_list