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Fix bug name_to_index dict #134

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merged 5 commits into from
Apr 6, 2021
Merged

Fix bug name_to_index dict #134

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a81633a
Merge pull request #127 from martimunicoy/devel
martimunicoy Feb 1, 2021
cf134d9
Fix name_to_index dict bug
laumalo Mar 16, 2021
7915079
Merge branch 'devel' of https://github.com/martimunicoy/peleffy into …
laumalo Mar 16, 2021
fb01aee
Merge branch 'devel' into fix_bug
laumalo Mar 16, 2021
9263e9b
Update releasehistory.rst
laumalo Mar 16, 2021
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1 change: 1 addition & 0 deletions docs/releasehistory.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
Bugfixes
""""""""
- `PR #129 <https://github.com/martimunicoy/peleffy/pull/129>`_: Some format errors in the API documentation are fixed. Links to the PELE documentation are updated.
- `PR #134 <https://github.com/martimunicoy/peleffy/pull/134>`_: Fixes bug when parsing the parameters of the ligand when OPLS is used to parameterize.


1.2.0 - New tools for parameters and templates
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28 changes: 14 additions & 14 deletions peleffy/forcefield/parameters.py
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Expand Up @@ -952,7 +952,7 @@ def from_ffld_output(molecule, ffld_output):
assert len(fields) > 7, 'Unexpected number of fields ' \
+ 'found at line {}'.format(line)

name_to_index[line[0:4]] = len(name_to_index)
name_to_index[line[0:8]] = len(name_to_index)

params['atom_types'].append(fields[3])
params['charges'].append(
Expand All @@ -971,8 +971,8 @@ def from_ffld_output(molecule, ffld_output):
+ 'found at line {}'.format(line)

params['bonds'].append(
{'atom1_idx': name_to_index[line[0:4]],
'atom2_idx': name_to_index[line[8:12]],
{'atom1_idx': name_to_index[line[0:8]],
'atom2_idx': name_to_index[line[8:16]],
'spring_constant': unit.Quantity(
float(fields[2]), unit.kilocalorie
/ (unit.angstrom ** 2 * unit.mole)),
Expand All @@ -986,9 +986,9 @@ def from_ffld_output(molecule, ffld_output):
+ 'found at line {}'.format(line)

params['angles'].append(
{'atom1_idx': name_to_index[line[0:4]],
'atom2_idx': name_to_index[line[8:12]],
'atom3_idx': name_to_index[line[16:20]],
{'atom1_idx': name_to_index[line[0:8]],
'atom2_idx': name_to_index[line[8:16]],
'atom3_idx': name_to_index[line[16:24]],
'spring_constant': unit.Quantity(
float(fields[3]), unit.kilocalorie
/ (unit.radian ** 2 * unit.mole)),
Expand All @@ -1001,10 +1001,10 @@ def from_ffld_output(molecule, ffld_output):
assert len(fields) > 9, 'Unexpected number of fields ' \
+ 'found at line {}'.format(line)

atom1_idx = name_to_index[line[0:4]]
atom2_idx = name_to_index[line[8:12]]
atom3_idx = name_to_index[line[16:20]]
atom4_idx = name_to_index[line[24:28]]
atom1_idx = name_to_index[line[0:8]]
atom2_idx = name_to_index[line[8:16]]
atom3_idx = name_to_index[line[16:24]]
atom4_idx = name_to_index[line[24:32]]

for k, periodicity, phase in zip(
fields[4:8], [1, 2, 3, 4],
Expand Down Expand Up @@ -1051,10 +1051,10 @@ def from_ffld_output(molecule, ffld_output):
unit.kilocalorie / unit.mole)

params['impropers'].append(
{'atom1_idx': name_to_index[line[0:4]],
'atom2_idx': name_to_index[line[8:12]],
'atom3_idx': name_to_index[line[16:20]],
'atom4_idx': name_to_index[line[24:28]],
{'atom1_idx': name_to_index[line[0:8]],
'atom2_idx': name_to_index[line[8:16]],
'atom3_idx': name_to_index[line[16:24]],
'atom4_idx': name_to_index[line[24:32]],
'periodicity': 2,
'phase': unit.Quantity(180.0, unit.degree),
'k': k / 2.0, # PELE works with half of Schrodinger's force constant
Expand Down