Commit ⋅ slochower/pAPRika

Showing 2 of 2 files from the diff.

paprika/tests/test_restraints.py changed.

@@ -1,7 +1,6 @@

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import logging

import numpy as np

from paprika.utils import override_dict

logger = logging.getLogger(__name__)

@@ -127,6 +126,15 @@

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    ):
        bias_type = "upper_walls"

    elif (
        amber_restraint_values["r2"] < amber_restraint_values["r3"]
        or amber_restraint_values["r2"] == 0.0
    ) and (
        amber_restraint_values["rk2"] <= amber_restraint_values["rk3"]
        or amber_restraint_values["rk2"] == 0.0
    ):
        bias_type = "upper_walls"

    elif (
        amber_restraint_values["r2"] > amber_restraint_values["r3"]
        or amber_restraint_values["r3"] == 0.0

@@ -139,6 +147,12 @@

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    ):
        bias_type = "lower_walls"

    elif (amber_restraint_values["r2"] < amber_restraint_values["r3"]) and (
        amber_restraint_values["rk2"] > amber_restraint_values["rk3"]
        or amber_restraint_values["rk3"] == 0.0
    ):
        bias_type = "lower_walls"

    if bias_type is None:
        raise Exception("Could not determine bias potential type from restraint.")


@@ -685,6 +685,30 @@

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    assert get_bias_potential_type(upper, "attach", 0) == "upper_walls"
    assert get_bias_potential_type(upper, "attach", 1) == "upper_walls"

    # Test upper wall restraint (3)
    upper = DAT_restraint()
    upper.auto_apr = False
    upper.amber_index = True
    upper.topology = os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl.pdb")
    upper.mask1 = "@K+"
    upper.mask2 = "@Cl-"

    upper.attach["fc_initial"] = 1.0
    upper.attach["fc_final"] = 1.0

    upper.custom_restraint_values["rk2"] = 0.0
    upper.custom_restraint_values["rk3"] = 1.0
    upper.custom_restraint_values["r2"] = 0.0
    upper.custom_restraint_values["r3"] = 3.5

    upper.attach["target"] = 3.5
    upper.attach["num_windows"] = len(attach_fractions)

    upper.initialize()

    assert get_bias_potential_type(upper, "attach", 0) == "upper_walls"
    assert get_bias_potential_type(upper, "attach", 1) == "upper_walls"

    # Test lower wall restraint (1)
    lower = DAT_restraint()
    lower.auto_apr = False

@@ -732,3 +756,27 @@

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732	756
733	757		assert get_bias_potential_type(lower, "attach", 0) == "lower_walls"
734	758		assert get_bias_potential_type(lower, "attach", 1) == "lower_walls"
	759	+
	760	+	# Test lower wall restraint (3)
	761	+	lower = DAT_restraint()
	762	+	lower.auto_apr = False
	763	+	lower.amber_index = True
	764	+	lower.topology = os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl.pdb")
	765	+	lower.mask1 = "@K+"
	766	+	lower.mask2 = "@Cl-"
	767	+
	768	+	lower.attach["fc_initial"] = 1.0
	769	+	lower.attach["fc_final"] = 1.0
	770	+
	771	+	lower.custom_restraint_values["rk2"] = 1.0
	772	+	lower.custom_restraint_values["rk3"] = 0.0
	773	+	lower.custom_restraint_values["r2"] = 3.5
	774	+	lower.custom_restraint_values["r3"] = 6.5
	775	+
	776	+	lower.attach["target"] = 3.5
	777	+	lower.attach["num_windows"] = len(attach_fractions)
	778	+
	779	+	lower.initialize()
	780	+
	781	+	assert get_bias_potential_type(lower, "attach", 0) == "lower_walls"
	782	+	assert get_bias_potential_type(lower, "attach", 1) == "lower_walls"

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setup.py	199	32	167	16.08%
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    project:
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  require_changes: false
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139	147		):
140	148		bias_type = "lower_walls"
141	149
	150	+	elif (amber_restraint_values["r2"] < amber_restraint_values["r3"]) and (
	151	+	amber_restraint_values["rk2"] > amber_restraint_values["rk3"]
	152	+	or amber_restraint_values["rk3"] == 0.0
	153	+	):
	154	+	bias_type = "lower_walls"
	155	+
142	156		if bias_type is None:
143	157		raise Exception("Could not determine bias potential type from restraint.")
144	158

685	685		assert get_bias_potential_type(upper, "attach", 0) == "upper_walls"
686	686		assert get_bias_potential_type(upper, "attach", 1) == "upper_walls"
687	687
	688	+	# Test upper wall restraint (3)
	689	+	upper = DAT_restraint()
	690	+	upper.auto_apr = False
	691	+	upper.amber_index = True
	692	+	upper.topology = os.path.join(os.path.dirname(__file__), "../data/k-cl/k-cl.pdb")
	693	+	upper.mask1 = "@K+"
	694	+	upper.mask2 = "@Cl-"
	695	+
	696	+	upper.attach["fc_initial"] = 1.0
	697	+	upper.attach["fc_final"] = 1.0
	698	+
	699	+	upper.custom_restraint_values["rk2"] = 0.0
	700	+	upper.custom_restraint_values["rk3"] = 1.0
	701	+	upper.custom_restraint_values["r2"] = 0.0
	702	+	upper.custom_restraint_values["r3"] = 3.5
	703	+
	704	+	upper.attach["target"] = 3.5
	705	+	upper.attach["num_windows"] = len(attach_fractions)
	706	+
	707	+	upper.initialize()
	708	+
	709	+	assert get_bias_potential_type(upper, "attach", 0) == "upper_walls"
	710	+	assert get_bias_potential_type(upper, "attach", 1) == "upper_walls"
	711	+
688	712		# Test lower wall restraint (1)
689	713		lower = DAT_restraint()
690	714		lower.auto_apr = False

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1	1		import logging
2	2
3	3		import numpy as np
4		-
5	4		from paprika.utils import override_dict
6	5
7	6		logger = logging.getLogger(__name__)

127	126		):
128	127		bias_type = "upper_walls"
129	128
	129	+	elif (
	130	+	amber_restraint_values["r2"] < amber_restraint_values["r3"]
	131	+	or amber_restraint_values["r2"] == 0.0
	132	+	) and (
	133	+	amber_restraint_values["rk2"] <= amber_restraint_values["rk3"]
	134	+	or amber_restraint_values["rk2"] == 0.0
	135	+	):
	136	+	bias_type = "upper_walls"
	137	+
130	138		elif (
131	139		amber_restraint_values["r2"] > amber_restraint_values["r3"]
132	140		or amber_restraint_values["r3"] == 0.0

1	# Codecov configuration to make it a bit less noisy
2	coverage:
3	status:
4	patch: false
5	project:
6	default:
7	threshold: 50%
8	comment:
9	layout: "header"
10	require_changes: false
11	branches: null
12	behavior: default
13	flags: null
14	paths: null