From 30dd54c9a38a83b825a5d80da39d667997aff502 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Tue, 4 Dec 2012 16:59:04 +0100
Subject: [PATCH] Changed value of bond_feasibility check for SLOPPY and CHARMM
profiles
Set bond_feasibility_check to True for SLOPPY and CHARMM profiles, kept
it to False for the STRICT profile
---
modules/io/doc/profile.rst | 4 ++--
modules/io/pymod/__init__.py | 6 ++++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/modules/io/doc/profile.rst b/modules/io/doc/profile.rst
index 9349b7c1c..82edfa484 100644
--- a/modules/io/doc/profile.rst
+++ b/modules/io/doc/profile.rst
@@ -55,7 +55,7 @@ SLOPPY:
IOProfile(dialect='PDB', strict_hydrogens=False, quack_mode=True,
fault_tolerant=True, join_spread_atom_records=False,
- no_hetatms=False, bond_feasibility_check=False)
+ no_hetatms=False, bond_feasibility_check=True)
CHARMM:
@@ -66,7 +66,7 @@ CHARMM:
IOProfile(dialect='CHARMM', strict_hydrogens=False, quack_mode=True,
fault_tolerant=True, join_spread_atom_records=True,
- no_hetatms=False, bond_feasibility_check=False)
+ no_hetatms=False, bond_feasibility_check=True)
The IOProfile Class
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index e9e597d72..abe1dcfdb 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -47,9 +47,11 @@ if not profiles:
profiles['STRICT']=IOProfile(dialect='PDB', fault_tolerant=False,
strict_hydrogens=False, quack_mode=False)
profiles['SLOPPY']=IOProfile(dialect='PDB', fault_tolerant=True,
- strict_hydrogens=False, quack_mode=True)
+ strict_hydrogens=False, quack_mode=True,
+ bond_feasibility_check=True)
profiles['CHARMM']=IOProfile(dialect='CHARMM', fault_tolerant=True,
- strict_hydrogens=False, quack_mode=False)
+ strict_hydrogens=False, quack_mode=False,
+ bond_feasibility_check=True)
profiles['DEFAULT']='STRICT'
def _override(val1, val2):
--
GitLab