Révision 5fb01677 modules/dos_input.py
| b/modules/dos_input.py | ||
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| 47 | 47 |
import logging |
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from configparser import ConfigParser, NoSectionError, NoOptionError, \ |
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MissingSectionHeaderError, DuplicateOptionError |
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import numpy as np |
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from modules.utilities import try_command |
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logger = logging.getLogger('DockOnSurf')
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| ... | ... | |
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def get_surf_norm_vect(): |
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import numpy as np |
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err = "'surf_norm_vect' must be either a 3 component vector or 'x', 'y' " \ |
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"or 'z'" |
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coords = {'x': [1.0, 0.0, 0.0],
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'y': [0.0, 1.0, 0.0],
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'z': [0.0, 0.0, 1.0]}
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cart_coords = {'x': [1.0, 0.0, 0.0], '-x': [-1.0, 0.0, 0.0],
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'y': [0.0, 1.0, 0.0], '-y': [0.0, -1.0, 0.0],
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'z': [0.0, 0.0, 1.0], '-z': [0.0, 0.0, -1.0]}
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surf_norm_vect_str = dos_inp.get('Screening', 'surf_norm_vect',
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fallback="0.0 0.0 1.0")
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fallback="z")
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if len(surf_norm_vect_str) == 1 and surf_norm_vect_str in coords:
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surf_norm_vect = coords[surf_norm_vect_str] |
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if surf_norm_vect_str in cart_coords:
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surf_norm_vect = cart_coords[surf_norm_vect_str]
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else: |
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surf_norm_vect = try_command(str2lst, [(ValueError, err)], |
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surf_norm_vect_str) |
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surf_norm_vect_str, float)
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if len(surf_norm_vect) != 3: |
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logger.error(err) |
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raise ValueError(err) |
| ... | ... | |
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return screen_rmsd |
| 524 | 524 |
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def get_coll_bottom():
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err_msg = num_error % ('collision_bottom', 'decimal number')
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coll_bottom = dos_inp.get('Screening', 'collision_bottom',
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fallback="False") |
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if coll_bottom.lower() in turn_false_answers:
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coll_bottom = False
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def get_min_coll_height():
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err_msg = num_error % ('min_coll_height', 'decimal number')
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min_coll_height = dos_inp.get('Screening', 'min_coll_height',
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fallback="False")
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if min_coll_height.lower() in turn_false_answers:
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min_coll_height = False
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else: |
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coll_bottom = try_command(float, [(ValueError, err_msg)], coll_bottom) |
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min_coll_height = try_command(float, [(ValueError, err_msg)], |
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min_coll_height) |
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return coll_bottom
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return min_coll_height
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def get_try_disso(): |
| ... | ... | |
| 678 | 679 |
return_vars['ads_algo'] = get_ads_algo() |
| 679 | 680 |
return_vars['sample_points_per_angle'] = get_pts_per_angle() |
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return_vars['collision_threshold'] = get_coll_thrsld() |
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return_vars['collision_bottom'] = get_coll_bottom() |
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return_vars['min_coll_height'] = get_min_coll_height() |
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cart_coords = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]] |
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if return_vars['min_coll_height'] is not False and \ |
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list(map(abs, return_vars['surf_norm_vect'].tolist())) not in \ |
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cart_coords: |
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logger.warning("'min_coll_height' option is only implemented for "
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"'surf_norm_vect' to be one of the x, y or z axes") |
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# Refinement |
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if refinement: |
Formats disponibles : Unified diff