"""
atomtools for geometry
"""
import os
import math
import itertools
import numpy as np
from numpy.linalg import norm
import modlog
import chemdata
BASEDIR = os.path.dirname(os.path.abspath(__file__))
EXTREME_SMALL = 1e-5
logger = modlog.getLogger(__name__)
def cos(theta, arc=False):
factor = 1 if arc else math.pi / 180.0
return math.cos(theta * factor)
def sin(theta, arc=False):
factor = 1 if arc else math.pi / 180.0
return math.sin(theta * factor)
def acos(result, arc=False):
factor = 1 if arc else 180.0 / math.pi
return math.acos(result) * factor
import os
import re
import argparse
import configparser
import modlog
from . import fileutil
BASE_DIR = os.path.dirname(os.path.abspath(__file__))
DEFAULT_FILETYPE_REGEXP_CONF = 'default_filetype.conf'
DEFAULT_FILETYPE_REGEXP_CONF = os.path.join(BASE_DIR,
DEFAULT_FILETYPE_REGEXP_CONF)
REG_ANYSTRING = r'[\s\S]*?'
FILETYPE_SECTION_NAME = 'filetype'
MULTIFRAME_NAME = 'multiframe'
logger = modlog.getLogger(__name__)
global FORMATS_REGEXP, MULTIFRAME
FORMATS_REGEXP, MULTIFRAME = dict(), list()
PARTIAL_LENGTH = 100000
def update_config(path=None):
global FORMATS_REGEXP, MULTIFRAME
path = path or DEFAULT_FILETYPE_REGEXP_CONF
if os.path.exists(path):
conf = configparser.ConfigParser(delimiters=('='))
conf.optionxform = str
conf.read(path)
FORMATS_REGEXP.update(conf._sections[FILETYPE_SECTION_NAME])
def set_loglevel(loglevel):
os.environ[LOGLEVEL_ENV] = str(loglevel)
main.logger = modlog.getLogger(main.__name__)
import modlog
logger = modlog.getLogger(__name__, 'color')
for level in ['debug', 'info', 'warn', 'error', 'critical']:
getattr(logger, level)(level)