Author: bugman
Date: Fri Mar 6 14:46:30 2009
New Revision: 8918
URL: http://svn.gna.org/viewcvs/relax?rev=8918&view=rev
Log:
All mol/res/spin naming and number user functions now accept the force arg.
Modified:
1.3/prompt/molecule.py
1.3/prompt/residue.py
1.3/prompt/spin.py
Modified: 1.3/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molecule.py?rev=8918&r1=8917&r2=8918&view=diff
==============================================================================
--- 1.3/prompt/molecule.py (original)
+++ 1.3/prompt/molecule.py Fri Mar 6 14:46:30 2009
@@ -206,7 +206,7 @@
display_molecule(mol_id=mol_id)
- def name(self, mol_id=None, name=None):
+ def name(self, mol_id=None, name=None, force=False):
"""Function for naming a molecule.
Keyword Arguments
@@ -215,6 +215,8 @@
mol_id: The molecule identification string corresponding to one or
more molecules.
name: The new molecule name.
+
+ force: A flag which if True will cause the molecule to be renamed.
Description
@@ -226,10 +228,10 @@
Examples
~~~~~~~~
- To rename the molecule 'Ap4Aase' to 'Inhib Ap4Aase', type:
-
- relax> molecule.name('#Ap4Aase', 'Inhib Ap4Aase')
- relax> molecule.name(mol_id='#Ap4Aase', name='Inhib Ap4Aase')
+ To rename the molecule 'Ap4Aase' to 'Inhib Ap4Aase', type one of:
+
+ relax> molecule.name('#Ap4Aase', 'Inhib Ap4Aase', True)
+ relax> molecule.name(mol_id='#Ap4Aase', name='Inhib Ap4Aase',
force=True)
This assumes the molecule 'Ap4Aase' already exists.
"""
@@ -238,7 +240,8 @@
if self.__relax__.interpreter.intro:
text = sys.ps3 + "molecule.name("
text = text + "mol_id=" + `mol_id`
- text = text + ", name=" + `name` + ")"
+ text = text + ", name=" + `name`
+ text = text + ", force=" + `force` + ")"
print text
# Residue identification string.
@@ -249,8 +252,12 @@
if type(name) != str:
raise RelaxStrError, ('new molecule name', name)
- # Execute the functional code.
- name_molecule(mol_id=mol_id, name=name)
+ # The force flag.
+ if type(force) != bool:
+ raise RelaxBoolError, ('force flag', force)
+
+ # Execute the functional code.
+ name_molecule(mol_id=mol_id, name=name, force=force)
Modified: 1.3/prompt/residue.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/residue.py?rev=8918&r1=8917&r2=8918&view=diff
==============================================================================
--- 1.3/prompt/residue.py (original)
+++ 1.3/prompt/residue.py Fri Mar 6 14:46:30 2009
@@ -230,7 +230,7 @@
display_residue(res_id=res_id)
- def name(self, res_id=None, name=None):
+ def name(self, res_id=None, name=None, force=False):
"""Function for naming residues.
Keyword Arguments
@@ -239,6 +239,8 @@
res_id: The residue identification string corresponding to one or
more residues.
name: The new name.
+
+ force: A flag which if True will cause the residue to be renamed.
Description
@@ -253,20 +255,21 @@
The following sequence of commands will rename the sequence {1 ALA,
2 GLY, 3 LYS} to {1 XXX,
2 XXX, 3 XXX}:
- relax> residue.name(':1', 'XXX')
- relax> residue.name(':2', 'XXX')
- relax> residue.name(':3', 'XXX')
+ relax> residue.name(':1', 'XXX', force=True)
+ relax> residue.name(':2', 'XXX', force=True)
+ relax> residue.name(':3', 'XXX', force=True)
Alternatively:
- relax> residue.name(':1,2,3', 'XXX')
+ relax> residue.name(':1,2,3', 'XXX', force=True)
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "residue.name("
text = text + "res_id=" + `res_id`
- text = text + ", name=" + `name` + ")"
+ text = text + ", name=" + `name`
+ text = text + ", force=" + `force` + ")"
print text
# Residue identification string.
@@ -277,11 +280,15 @@
if type(name) != str:
raise RelaxStrError, ('new residue name', name)
- # Execute the functional code.
- name_residue(res_id=res_id, name=name)
-
-
- def number(self, res_id=None, number=None):
+ # The force flag.
+ if type(force) != bool:
+ raise RelaxBoolError, ('force flag', force)
+
+ # Execute the functional code.
+ name_residue(res_id=res_id, name=name, force=force)
+
+
+ def number(self, res_id=None, number=None, force=False):
"""Function for numbering residues.
Keyword Arguments
@@ -290,6 +297,8 @@
res_id: The residue identification string corresponding to a single
residue.
number: The new residue number.
+
+ force: A flag which if True will cause the residue to be renumbered.
Description
@@ -305,16 +314,17 @@
The following sequence of commands will renumber the sequence {1
ALA, 2 GLY, 3 LYS} to
{101 ALA, 102 GLY, 103 LYS}:
- relax> residue.number(':1', 101)
- relax> residue.number(':2', 102)
- relax> residue.number(':3', 103)
+ relax> residue.number(':1', 101, force=True)
+ relax> residue.number(':2', 102, force=True)
+ relax> residue.number(':3', 103, force=True)
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "residue.number("
text = text + "res_id=" + `res_id`
- text = text + ", number=" + `number` + ")"
+ text = text + ", number=" + `number`
+ text = text + ", force=" + `force` + ")"
print text
# Residue identification string.
@@ -325,8 +335,12 @@
if type(number) != int:
raise RelaxIntError, ('new residue number', number)
- # Execute the functional code.
- number_residue(res_id=res_id, number=number)
+ # The force flag.
+ if type(force) != bool:
+ raise RelaxBoolError, ('force flag', force)
+
+ # Execute the functional code.
+ number_residue(res_id=res_id, number=number, force=force)
Modified: 1.3/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/spin.py?rev=8918&r1=8917&r2=8918&view=diff
==============================================================================
--- 1.3/prompt/spin.py (original)
+++ 1.3/prompt/spin.py Fri Mar 6 14:46:30 2009
@@ -225,7 +225,7 @@
display_spin(spin_id=spin_id)
- def name(self, spin_id=None, name=None):
+ def name(self, spin_id=None, name=None, force=False):
"""Function for naming spins.
Keyword Arguments
@@ -234,6 +234,8 @@
spin_id: The spin identification string corresponding to one or
more spins.
name: The new name.
+
+ force: A flag which if True will cause the spin to be renamed.
Description
@@ -248,16 +250,17 @@
The following sequence of commands will rename the sequence {1 C1, 2
C2, 3 C3} to {1 C11,
2 C12, 3 C13}:
- relax> spin.name('@1', 'C11')
- relax> spin.name('@2', 'C12')
- relax> spin.name('@3', 'C13')
+ relax> spin.name('@1', 'C11', force=True)
+ relax> spin.name('@2', 'C12', force=True)
+ relax> spin.name('@3', 'C13', force=True)
"""
# Function intro text.
if self.__relax__.interpreter.intro:
text = sys.ps3 + "spin.name("
text = text + "spin_id=" + `spin_id`
- text = text + ", name=" + `name` + ")"
+ text = text + ", name=" + `name`
+ text = text + ", force=" + `force` + ")"
print text
# Spin identification string.
@@ -268,11 +271,15 @@
if type(name) != str:
raise RelaxStrError, ('new spin name', name)
- # Execute the functional code.
- name_spin(spin_id=spin_id, name=name)
-
-
- def number(self, spin_id=None, number=None):
+ # The force flag.
+ if type(force) != bool:
+ raise RelaxBoolError, ('force flag', force)
+
+ # Execute the functional code.
+ name_spin(spin_id=spin_id, name=name, force=force)
+
+
+ def number(self, spin_id=None, number=None, force=False):
"""Function for numbering spins.
Keyword Arguments
@@ -281,6 +288,8 @@
spin_id: The spin identification string corresponding to a single
spin.
number: The new spin number.
+
+ force: A flag which if True will cause the spin to be renumbered.
Description
@@ -296,9 +305,9 @@
The following sequence of commands will renumber the sequence {1 C1,
2 C2, 3 C3} to
{-1 C1, -2 C2, -3 C3}:
- relax> spin.number('@1', -1)
- relax> spin.number('@2', -2)
- relax> spin.number('@3', -3)
+ relax> spin.number('@1', -1, force=True)
+ relax> spin.number('@2', -2, force=True)
+ relax> spin.number('@3', -3, force=True)
"""
@@ -306,7 +315,8 @@
if self.__relax__.interpreter.intro:
text = sys.ps3 + "spin.number("
text = text + "spin_id=" + `spin_id`
- text = text + ", number=" + `number` + ")"
+ text = text + ", number=" + `number`
+ text = text + ", force=" + `force` + ")"
print text
# Spin identification string.
@@ -317,8 +327,12 @@
if number != None and type(number) != int:
raise RelaxNoneIntError, ('new spin number', number)
- # Execute the functional code.
- number_spin(spin_id=spin_id, number=number)
+ # The force flag.
+ if type(force) != bool:
+ raise RelaxBoolError, ('force flag', force)
+
+ # Execute the functional code.
+ number_spin(spin_id=spin_id, number=number, force=force)
r8918 - in /1.3/prompt: molecule.py residue.py spin.py