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Merge pull request #6 from schrodinger/titrate_only

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Titrate only option
This commit is contained in:
Jimmy Charnley Kromann
2014-08-27 14:53:54 +02:00
parent b617175f77 8084b31393
commit 6e1b0365e0
5 changed files with 114 additions and 31 deletions
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40
Tests/runtest.py
View File

@@ -10,19 +10,37 @@ import os, re
import sys
if __name__ == "__main__":
pdbs = ['1FTJ-Chain-A',
'1HPX',
'4DFR']
# A list of input structures and command-line arguments to be passed in
# to PROPKA for each:
pdbs = [('1FTJ-Chain-A', []),
('1HPX', []),
('4DFR', []),
('3SGB', []),
('3SGB-subset', ['--titrate_only', 'E:17,E:18,E:19,E:29,E:44,E:45,E:46,E:118,E:119,E:120,E:139']),
]
for pdb in pdbs:
for pdb, args in pdbs:
print('')
print('RUNNING '+pdb)
# Run pka calculation
call([sys.executable, '../scripts/propka31.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
fh = open(pdb + '.out', 'w')
cmd = [sys.executable, '../scripts/propka31.py','pdb/%s.pdb' % pdb] + args
ret = call(cmd, stdout=fh, stderr=fh)
if ret != 0:
print(" ERR:")
print(" Failed to execute PROPKA on %s" % pdb)
print(" See: %s.out" % pdb)
sys.exit(1)
# Test pka predictiona
result = open('results/'+pdb+'.dat','r')
# Test pka predictions
result_file = 'results/%s.dat' % pdb
if not os.path.isfile(result_file):
print(" ERR:")
print(" file not found: %s" % result_file)
sys.exit(1)
result = open(result_file,'r')
atpka = False
for line in open(pdb+'.pka', 'r').readlines():
if not atpka:
@@ -37,11 +55,13 @@ if __name__ == "__main__":
atpka = False
continue
r = float(result.readline())
expected_value = float(result.readline())
m = re.search('([0-9]+\.[0-9]+)', line)
value = float(m.group(0))
if(float(m.group(0)) != r):
if value != expected_value:
print(" ERR:")
print(line)
print(" "+"should be: "+str(r))
print(" %s should be: %s" % (value, expected_value))
sys.exit(1)

49
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
@@ -74,8 +76,7 @@ class Conformation_container:
def find_covalently_coupled_groups(self):
""" Finds covalently coupled groups and sets common charge centres if needed """
for group in [ group for group in self.groups if group.titratable]:
for group in self.get_titratable_groups():
# Find covalently bonded groups
bonded_groups = self.find_bonded_titratable_groups(group.atom, 1, group.atom)
@@ -131,8 +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
@@ -140,18 +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
#
@@ -335,8 +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

12
propka/group.py
View File

@@ -338,6 +338,7 @@ class Group:
res.covalently_coupled_groups = self.covalently_coupled_groups
res.non_covalently_coupled_groups = self.non_covalently_coupled_groups
res.titratable = self.titratable
res.exclude_cys_from_results = self.exclude_cys_from_results
res.charge = self.charge
return res
@@ -367,7 +368,7 @@ class Group:
if self.model_pka_set and not self.atom.cysteine_bridge:
self.titratable = True
self.exclude_cys_from_results = False
return
@@ -606,6 +607,15 @@ class Group:
return charge
def use_in_calculations(self):
"""
Whether this group should be included in the 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 self.titratable or (self.residue_type == 'CYS' and \
not self.exclude_cys_from_results)
class COO_group(Group):

41
propka/lib.py
View File

@@ -75,6 +75,29 @@ def make_combination(combis, interaction):
return res
def parse_res_string(res_str):
"""
Parse the residue string, in format "chain:resnum[inscode]", and return
a tuple of (chain, resnum, inscode). Raises ValueError if the input
string is invalid.
"""
try:
chain, resnum_str = res_str.split(":")
except ValueError:
raise ValueError("Invalid residue string (must contain 2 colon-separated values)")
try:
resnum = int(resnum_str)
except ValueError:
try:
resnum = int(resnum_str[:-1])
except ValueError:
raise ValueError("Invalid residue number (not an int)")
else:
inscode = resnum_str[-1]
else:
inscode = " "
return chain, resnum, inscode
def loadOptions():
"""
@@ -94,7 +117,11 @@ def loadOptions():
parser.add_option("-r", "--reference", dest="reference", default="neutral",
help="setting which reference to use for stability calculations [neutral/low-pH]")
parser.add_option("-c", "--chain", action="append", dest="chains",
help="creating the protein with only a specified chain, note, chains without ID are labeled 'A' [all]")
help='creating the protein with only a specified chain. Specify " " for chains without ID [all]')
parser.add_option("-i", "--titrate_only", dest="titrate_only",
help='Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for example: '
'-i "A:10,A:11"')
parser.add_option("-t", "--thermophile", action="append", dest="thermophiles",
help="defining a thermophile filename; usually used in 'alignment-mutations'")
parser.add_option("-a", "--alignment", action="append", dest="alignment",
@@ -147,7 +174,17 @@ def loadOptions():
print("Warning: no pdbfile provided")
#sys.exit(9)
# Convert titrate_only string to a list of (chain, resnum) items:
if options.titrate_only is not None:
res_list = []
for res_str in options.titrate_only.split(','):
try:
chain, resnum, inscode = parse_res_string(res_str)
except ValueError:
print('Invalid residue string: "%s"' % res_str)
sys.exit(1)
res_list.append((chain, resnum, inscode))
options.titrate_only = res_list
# done!
return options, args

3
propka/molecular_container.py
View File

@@ -139,7 +139,8 @@ class Molecular_container:
parameters=self.conformations[self.conformation_names[0]].parameters,
molecular_container=self)
for group in self.conformations[self.conformation_names[0]].get_titratable_groups_and_cysteine_bridges():
container = self.conformations[self.conformation_names[0]]
for group in container.get_groups_for_calculations():
# new group to hold average values
avr_group = group.clone()
# sum up all groups ...