schrodinger.application.matsci.automated_martini_mapping_protein module¶

Map an all-atom protein structure to a coarse-grained one compatible with the Martini force field.

exception schrodinger.application.matsci.automated_martini_mapping_protein.OverlapError¶

Bases: Exception

Error to raise when an atom is found in two different residue matches

exception schrodinger.application.matsci.automated_martini_mapping_protein.MissingAtoms¶

Bases: Exception

Exception raised when mapping fails.

exception schrodinger.application.matsci.automated_martini_mapping_protein.MissingSecondaryStructure¶

Bases: Exception

Exception raised when secondary structure is missing.

class schrodinger.application.matsci.automated_martini_mapping_protein.CGStructBuilder(aa_struct, mapping_info)¶

Bases: object

Create a coarse-grained structure based on all-atom structure’s mapping

__init__(aa_struct, mapping_info)¶

Create an instance.

Parameters:

aa_struct (structure.Structure) – The all-atom structure
mapping_info (dict) – The protin’s martini mapping information

createCGStruct(all_hits)¶

Create a coarse-grained structure.

Parameters:: all_hits (dict) – The mapping information
Return type:: structure.Structure
Returns:: The coarse-grained structure

addBackmapping(caps, mapped_atoms)¶

Record parent AA information on CG structure to aid in future reconstruction of the AA structure from the CG structure. Per each CG site type, store AA structure extract as CG structure property and record bonding information in CG particle atom properties. Also record as structure property the structure and bonding of terminal capping groups not corresponding to any particle.

Parameters:

caps (dict) – Collection of the capping groups
mapped_atoms (dict) – Mappings of the CG particle index to the corresponding AA atom index

findCapNeighbors(caps, mapped_atoms)¶

Find the neighbors of the capping groups. Add the capping group information to the coarse-grained structure.

Parameters:

caps (dict) – Collection of the capping groups
mapped_atoms (dict) – Mappings of the CG particle index to the

Return type:

list(tuple)

Returns:

Contains the capping group and its neighbor particle atom name

adjustHelixTerminal()¶: Correct for Martini’s use of slightly different site types for terminal neutral backbone sites in helices.

findNTerminae()¶

Find the N-termini of the CG structure.

Return type:: list(structure.Atom)
Returns:: Contains the N-terminal atoms of the CG structure

findCTerminae()¶

Find the C-termini of the CG structure.

Return type:: list(structure.Atom)
Returns:: Contains the C-terminal atoms of the CG structure

static findBackboneChains(cg_struct)¶

Find the backbone chains in the CG structure.

Parameters:: cg_struct (structure.Structure) – The coarse-grained structure
Return type:: list(list(structure.Atom))
Returns:: Contains the backbone chains in the CG structure

addNewSite(a_site, site_info, a_match, a_residue, atom_idx, mapped_atoms, internal_sites)¶

Add a new site to the coarse-grained structure.

Parameters:

a_site (str) – The site type
site_info (dict) – The site information from the mapping json file
a_residue (str) – Residue name as key from the json file
a_match (list(int)) – The atom indices from the AA structure matching to the site type SMARTS pattern
atom_idx (int) – The atom index from the AA structure
mapped_atoms (dict) – Mappings of the CG particle index to the corresponding AA atom index
internal_sites (dict) – The internal bonds for the site

createNewSite(atom_idx, a_residue, a_residue_info, a_match, mapped_atoms, caps)¶

Create a new site in the coarse-grained structure.

Parameters:

atom_idx (int) – The atom index from the AA structure
a_residue (str) – Residue name as key from the json file
a_residue_info (dict) – Contains residue SMARTS pattern, external bonding information, site mappings, colors, and names for different bead types.
a_match (list(int)) – The atom indices from the AA structure matching to the site type SMARTS pattern
mapped_atoms (dict) – Mappings of the CG particle index to the corresponding AA atom index
caps (dict) – Collection of the capping groups

Return type:

list

Returns:

atoms which should not be mapped if mapped particle is Nothing

addBonds(a_residue_info, a_match, mapped_atoms, internal_sites)¶

Add bonds to the coarse-grained structure.

Parameters:

a_residue_info (dict) – residue information from the mapping json file
a_match (list(int)) – The atom indices from the AA structure
mapped_atoms (dict) – Mappings of the CG particle index to the
internal_sites (dict) – The internal bonds for the site

static getCutBonds(aa_struct, parent_atoms)¶

Collect the bonds of parent atoms that are cut, because of CG mapping.

Parameters:

aa_struct (structure.Structure) – The all-atom structure
parent_atoms (list) – The parent atoms

Return type:

list(tuple(int, int, int))

Returns:

list of AA bonds that are cut

getCommonValueProp(parent_atoms, property_name)¶

Find the most common value of a property among parent atoms.

Parameters:

parent_atoms (list) – The parent atoms
property_name (str) – The property name

Return type:

str

Returns:

The most common value of the property among parent atoms

class schrodinger.application.matsci.automated_martini_mapping_protein.Mapper(mapping_info, aa_struct)¶

Bases: object

Mapper class to find mapping between all-atom and coarse-grained structures.

__init__(mapping_info, aa_struct)¶

Create an instance.

Parameters:

mapping_info (dict) – The protein’s Martini mapping information
aa_struct (structure.Structure) – The all-atom structure

determineMapping()¶

Determine the mapping, using the Martini mapping information.

Return type:: dict
Returns:: The mapping information as a dictionary of atom index and the residue name, residue info, and match that the atom is in

cleanHTerminals()¶: Clean unmapped H atoms bound to the N terminal N atom of a protein backbone

storeMatchingHits()¶

Store matched atoms in a dictionary.

Raises:: OverlapError – If an atom is found in two different residue matches
Return type:: dict
Returns:: A dictionary of atom index and the residue, residue info, and match that the atom is in

checkMatchesContained()¶: Find matches that are subsets of other matches and eliminate them.

static convertAlternateHtoCaps(res_info, H_Nterminal_info)¶

For most residues in chain the N terminus would be R’-NH-R’’ and the SMARTS patterns have only 1 H on the terminal N. This leads to two matches for the same residue but involving different H atoms. This function removes one of the two matches for backbone N terminations with NH2-R for proteins and places the unmapped hydrogen into a new unmapped group for backmapping

Parameters:

res_info (dict) – information on a residue
H_Nterminal_info (dict) – information on unmapped H atoms for terminal

static removeFirstH(res_info, H_Nterminal_info)¶

For most Proline residues in a chain the N terminus would be R’-N(-R’’)-R’’’ and the SMARTS patterns have no H on the terminal N. For prolines at the N terminus of a protein backbone chain sometimes this site is neutral (i.e., there is an H on the N atom) and this can lead to an unmapped H atom. A pattern has been added for such proleins and they map onto normal PRO Martini sites. The unmapped H atom needs to be tracked for recording backmapping information.

Parameters:

a_residue_info (dict) – info on a N-terminal PRO residue
H_Nterminal_info (dict) – info on unmapped H atoms for terminal residues

class schrodinger.application.matsci.automated_martini_mapping_protein.AutomatedMartiniProteinMapping(struct, keep_secondary_structure=True)¶

Bases: object

Class to map an AA structure to a CG structure using the Martini mapping defined for protein residues.

MULTI_MOL = 1¶

__init__(struct, keep_secondary_structure=True)¶

Generate the CG structure from the AA structure. Using the residues in the mapping file, search the AA structure for matches, map the AA atom indices to a CG particle, generate and store the particles in a CG structure.

Parameters:

struct (structure.Structure) – the AA structure to be coarse grained
keep_secondary_structure (bool) – retain the input protein secondary structure or not. Default is True.

Return type:

structure.Structure

Returns:

The CG structure

map()¶

Map the AA structure to the CG structure

Return type:: structure.Structure
Returns:: The CG structure

tagAAStructure()¶: Tag the AA structure with the CG structure’s information.

class schrodinger.application.matsci.automated_martini_mapping_protein.StructuralHarmonicRestraints(struct, force_constant=3.585, target_distance=10.0)¶

Bases: object

Class to generate harmonic restraints on the protein backbone atoms

STRANDS_FC_KEY = 'force_constant'¶

STRANDS_MIN_ANGLE_KEY = 'minimum_angle'¶

STRANDS_APPLY_KEY = 'apply'¶

MOL_GROUPS_KEY = 'groups'¶

STRAND_RESTRAINTS_KEY = 'strand_restraints'¶

EXCLUDE_RESTRAINTS_KEY = 'exclude_restaints_between_group_of_sites'¶

EXTRA_SITES_RESTRAINTS_KEY = 'restrain_other_sites_in_protein_molecules'¶

GROUP_MEMBERS_KEY = 'group_members'¶

ATOMI_KEY = 'atom_i'¶

ATOMJ_KEY = 'atom_j'¶

DIST_KEY = 'distance'¶

FC_KEY = 'fc'¶

REST_BLOCK_SEP = ';'¶

REST_PARAM_SEP = ','¶

DEFAULT_FC = 3.585¶

DEFAULT_RC = 10.0¶

STRAND_TURN = 'strand_turn'¶

__init__(struct, force_constant=3.585, target_distance=10.0)¶

Generate harmonic restraints on the protein backbone atoms

Parameters:

struct (structure.Structure) – input cg structure
force_constant (float) – harmonic restraints’ force constant (kcal/mol/A^2)
target_distance (float) – largest distance (A) between backbone protein particles to be restrained

addHarmonicRestraints()¶

Add harmonic restraints to the protein based on the restraints defined in the json file

Return type:: structure.Structure
Returns:: The CG structure with restraints added as atom properties

createRestraints()¶: Create the harmonic restraints

storeRestraintsOnStruct()¶: Store the restraints on the structure as atom properties

otherRestraints(mol, backbone)¶: Create the harmonic restraints for other particles that are not part of the backbone or a strand

strandRestraints(backbone)¶: Create the harmonic restraints for the strands. In principle there should be a dihedral potential between side_chain(i)-backbone(i)-backbone(i+1)-side_chain(i+1) particles at the input geometry. Dihedrals were problematic when this was implemented so a distance restraint is applied between the input side chain particles to maintain the current geometry. This restraint is problematic if the dihedral angle is less than a certain value. The minimum_angle specifies this value and dihedrals less than this value are not restrained.

sideChainS1(atom)¶

Find the side chain S1 atom for the given atom index

Parameters:: atom (structure.Atom) – The atom
Return type:: schrodinger.structure.atom.Atom or None
Returns:: The side chain S1 atom, or None if not found

backboneRestraints(backbone)¶

Create the harmonic restraints between backbone particles

Parameters:: backbone (list) – The backbone atoms

isInExcludedGroups(atom1_idx, atom2_idx)¶

Check if the atoms are supposed to be excluded from the restraints

Parameters:

atom1_idx (int) – The first atom index
atom2_idx (int) – The second atom index

Return type:

bool

Returns:

True if the atoms are supposed to be excluded

restraintBlock(atom1_idx, atom2_idx, distance, k_spring)¶

Create a restraint block

Parameters:

atom1_idx (int) – The first atom index
atom2_idx (int) – The second atom index
distance (float) – The distance (A)
k_spring (float) – The force constant (kcal/mol/A^2)

Return type:

dict

Returns:

The restraint block

addSingleRestraint(atom1, atom2, dist=None, k_spring=None, check_exclusion=True, check_distance_target=True)¶

Create a single restraint between two atoms

Parameters:

atom1 (structure.Atom) – The first atom
atom2 (structure.Atom) – The second atom
dist (float) – The distance (A). If None, calculate from structure
k_spring (float) – The force constant (kcal/mol/A^2). If None, assigned by default
check_exclusion (bool) – Check if the atoms are supposed to be excluded from the restraints
check_distance_target (bool) – Check if the distance is within the target distance

Return type:

list

Returns:

The restraint between the two atoms

backbone(molecule)¶

Find the backbone atoms in the protein

Parameters:: molecule (structure.Molecule) – The molecule
Return type:: list(schrodinger.structure.atom.Atom)
Returns:: The backbone atoms

excludedGroups(set_of_groups)¶

Find the groups to exclude from the restraints

Parameters:: set_of_groups (dict) – The set of groups to exclude
Return type:: list
Returns:: The groups to exclude