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.MissingSecondaryStructure¶

Bases: Exception

Exception raised when secondary structure is missing.

exception schrodinger.application.matsci.automated_martini_mapping_protein.AdditionalRestraintsError¶

Bases: Exception

Exception raised when additional restraints cannot be applied.

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

Bases: object

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

class PARTICLE_INFO(atom_idxs, cen_on_idxs, color, charge, bond_id, resid, parent_chain_name, parent_residue_num, parent_residue_name, parent_mapped_resname)¶

Bases: tuple

atom_idxs¶: Alias for field number 0

bond_id¶: Alias for field number 4

cen_on_idxs¶: Alias for field number 1

charge¶: Alias for field number 3

color¶: Alias for field number 2

parent_chain_name¶: Alias for field number 6

parent_mapped_resname¶: Alias for field number 9

parent_residue_name¶: Alias for field number 8

parent_residue_num¶: Alias for field number 7

resid¶: Alias for field number 5

__init__(residues_info, aa_struct)¶

Create an instance.

Parameters:

residues_info (dict) – The protein’s Martini mapping information per residue type.
aa_struct (Structure) – The all-atom structure

determineMapping()¶: Determine the mapping, using the Martini mapping information.

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

defineParticles()¶: Define the particles based on mapping information from the residues.

processBonds()¶: Process the internal bonds information from the json file. Assign a bond index to every site in the definition of a residue. Matching bond indexes will be used to identify pairs that should be bonded, after particles are defined.

getAParticle(a_match, a_site, site_info, resname)¶

Get the particle information for a match.

Parameters:

a_match (list(int)) – The atom indices of the match
a_site (str) – The site name from json mapping file
site_info (dict) – The mapping info for the given site from json file
res_info (dict) – The residue information from json mapping file

Return type:

tuple(str, int, PARTICLE_INFO)

Returns:

The particle name, number, and self.PARTICLE_INFO object storing the particle information

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

storeCaps(a_match, a_site, site_info, res_info)¶

Store the capping atoms information.

Parameters:

a_match (list) – The atom indices of the match
a_site (str) – The site name from json mapping file
site_info (dict) – The site information from json mapping file
res_info (dict) – The residue information from json mapping file

static particleNameAndColor(a_site, site_info, a_atom)¶

Get the particle name based on the site type.

Parameters:

a_site (str) – The site name
site_info (dict) – The site information
a_atom (Structure) – An atom corresponding to this site

Return type:

tuple(str, str)

Returns:

The particle name and its color

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)¶

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)¶

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) – the AA structure to be coarse grained
Return type:: Structure
Returns:: The CG structure

map()¶

Map the AA structure to the CG structure

Return type:: Structure
Returns:: The AA structure that is tagged with the CG mapping information

mapAAStructure(mapped_particles, cap_atoms, ignored_atoms)¶

Map the AA structure to the CG structure using the mapped particles.

Parameters:

mapped_particles (dict) – The particles mapping information
cap_atoms (dict) – The capping atoms information
ignored_atoms (list[atom]) – The atoms that are not mapped to any particle

addAtomProp(atom_idxs, props_values)¶

Add the other atom properties to the AA structure.

Parameters:

atom_idxs (list) – The atom indices to add the property to
props_values (dict) – The properties the their values to add to each atom

addCappingStructProperties(cap_atoms)¶

Add the capping properties to the AA structure.

Parameters:: cap_atoms (dict) – The capping atoms information

addParticleInfo(name, group, pattern, charge)¶

Add the particle information to the particles_info list.

Parameters:

name (str) – The particle name
group (list) – The atom indices of the particle in the AA structure
pattern (Pattern) – The pattern to convert the atom indices to a SMARTS pattern
charge (int) – The particle charge

addMappingAtomProperties(name, num, group)¶

Add the mapping properties to the AA structure.

Parameters:

name (str) – The particle name
num (int) – The particle number
group (list) – The atom indices of the particle in the AA structure

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) – 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

static isProtMapped(struct)¶

Check if the structure is a mapped protein structure.

Parameters:: struct (Structure) – The structure to check
Return type:: bool
Returns:: True if the structure is a mapped protein structure

addRelativeBackboneSiteProperties()¶: Add the previous backbone site property to each backbone atom in the structure.

addHarmonicRestraints()¶

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

Return type:: 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