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#! /usr/bin/env python3
#
# Copyright 2009-2024 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
import lxml.etree as lxml
import re
import argparse
VERSION = '@PROJECT_VERSION@ #VOTCA_GIT_ID#'
PROGTITLE = 'THE VOTCA::XTP MAPPING FILE UPDATER'
PROGDESCR = 'Updates the CTP mapping file to VOTCA XTP'
VOTCAHEADER = '''\
==================================================
======== VOTCA (http://www.votca.org) ========
==================================================
{progtitle}
please read and cite: @PROJECT_CITATION@
and submit bugs to @PROJECT_CONTACT@
xtp_update_mapfile, version {version}
'''.format(version=VERSION, progtitle=PROGTITLE)
# =============================================================================
# PROGRAM OPTIONS
# =============================================================================
class XtpHelpFormatter(argparse.HelpFormatter):
def _format_usage(self, usage, action, group, prefix):
return VOTCAHEADER
progargs = argparse.ArgumentParser(prog='xtp_update_mapfile',
formatter_class=lambda prog: XtpHelpFormatter(
prog, max_help_position=70),
description=PROGDESCR)
progargs.add_argument('-sin', '--S_input',
dest='S_input',
required=True,
type=argparse.FileType('r'),
default='',
help='Mapping file to update.')
progargs.add_argument('-sout', '--S_output',
dest='S_output',
required=True,
type=argparse.FileType('w'),
default='',
help='Filename of new Mapping file.')
OPTIONS = progargs.parse_args()
# =============================================================================
# LXML
# =============================================================================
def RepresentsInt(s):
try:
int(s)
return True
except ValueError:
return False
def changeframe(localframetext):
ids = localframetext.split()
newids = []
for i in ids:
if RepresentsInt(i):
integer = int(i)
else:
print("Cannot convert {} to integer".format(i))
newinteger = integer - 1
newids.append("{:d}".format(newinteger))
return ' '.join(newids)
def changeids(atomidtext):
re_s = re.compile(r'(\S+)')
atoms_and_whitespaces = re_s.split(atomidtext)
newstring = []
for atom in atoms_and_whitespaces:
if not atom or atom.isspace():
newstring.append(atom)
else:
array = atom.split(":")
atomtype = array[1]
if RepresentsInt(array[0]):
integer = int(array[0])
else:
print("Cannot convert {} to integer".format(array[0]))
newinteger = integer - 1
newstring.append(f"{newinteger}:{atomtype}")
return ''.join(newstring)
print("Reading in {}".format(OPTIONS.S_input.name))
Tree = lxml.parse(OPTIONS.S_input.name)
Root = Tree.getroot()
Molecules = Root.find("molecules")
for molecule in Molecules.iter('molecule'):
segments = molecule.find("segments")
for segment in segments.iter('segment'):
fragments = segment.find("fragments")
for fragment in fragments.iter('fragment'):
qmatoms = fragment.find("qmatoms")
qmatoms.text = changeids(qmatoms.text)
mpoles = fragment.find("mpoles")
mpoles.text = changeids(mpoles.text)
localframe = fragment.find("localframe")
localframe.text = changeframe(localframe.text)
print("Writing to {}".format(OPTIONS.S_output.name))
Tree.write(OPTIONS.S_output.name, pretty_print=True)
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