From 893d5f40bdf2b55b6975842333cbe396c833a6af Mon Sep 17 00:00:00 2001 From: James Krieger Date: Wed, 2 Nov 2022 17:07:15 +0100 Subject: [PATCH 1/2] fix pdb parser --- continuousflex/protocols/utilities/pdb_parser.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/continuousflex/protocols/utilities/pdb_parser.py b/continuousflex/protocols/utilities/pdb_parser.py index ae0ebc8..9c046b9 100644 --- a/continuousflex/protocols/utilities/pdb_parser.py +++ b/continuousflex/protocols/utilities/pdb_parser.py @@ -86,7 +86,7 @@ def m_inout_read_pdb(filename): pdb_list = [] f = open(filename, 'r') for line in f: - test_recd = line[0:5] + test_recd = line[:6] # if test_recd.upper().strip() == "ATOM" or test_recd.upper() == "HETATM": if ((test_recd.upper().strip() == "ATOM") or (test_recd.upper().strip() == "HETATM")): @@ -98,19 +98,19 @@ def m_inout_read_pdb(filename): except: pass try: - new_atom.type = line[12:14] - except: - pass - try: - new_atom.loc = line[14:16] + new_atom.type = line[11:15] except: pass + # try: + # new_atom.loc = line[14:16] + # except: + # pass try: new_atom.alt = line[16] except: pass try: - new_atom.res = line[17:21] + new_atom.res = line[17:20] except: pass try: From 87394db8b33aae5f43b3c5a7a8e2a4cfffe8a04c Mon Sep 17 00:00:00 2001 From: James Krieger Date: Wed, 2 Nov 2022 18:41:40 +0100 Subject: [PATCH 2/2] use icode for 5-digit seq --- .../protocols/utilities/pdb_parser.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/continuousflex/protocols/utilities/pdb_parser.py b/continuousflex/protocols/utilities/pdb_parser.py index 9c046b9..c4790e9 100644 --- a/continuousflex/protocols/utilities/pdb_parser.py +++ b/continuousflex/protocols/utilities/pdb_parser.py @@ -117,14 +117,19 @@ def m_inout_read_pdb(filename): new_atom.chain = line[21] except: pass + try: - new_atom.seq = int(line[22:26]) + new_atom.seq = int(line[23:27]) except: - pass - try: - new_atom.icode = line[26] - except: - pass + try: + new_atom.seq = int(line[23:26]) + except: + pass + try: + new_atom.icode = line[26] + except: + pass + try: new_atom.x = float(line[30:38]) except: